The trouble codes LS swaps actually set, what each one means, the swap causes to check first (cheapest and most likely at the top), and whether it can be turned off in the tune.
Turning codes off. We only turn off codes for parts a swap legitimately doesn't have: MAF codes on speed density, the anti-theft codes when you ask for VATS off, an automatic's codes behind a manual, and a missing transmission or body module on request. That's 19 codes, each one listed in your change log. Emissions codes (catalyst, oxygen sensors, EVAP, misfire, fuel trim, thermostat) are never turned off: on a street car that's tampering. We explain them and fix the cause. Everything else is the computer telling you something real.
Crank, cam and no-start
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Crank position sensor (circuit / range-performance)
P0335P0336Fix the cause
The computer isn't getting a clean crank signal. No crank signal means no fuel and no spark, so it usually cranks and never fires.
Likely on a swap (check in this order)
Crank sensor, reluctor and computer don't match: 24x (Gen III) or 58x (Gen IV). A 58x engine on a 24x computer, or the reverse, cranks strong and never fires.
Wrong sensor for the engine. A black connector usually means 24x and gray 58x (a hint, not proof). A 58x engine needs the gray sensor; a quality sensor beats a bargain one.
No power or ground at the sensor connector (12 V on a 24x sensor, 5 V on a 58x sensor).
A damaged reluctor wheel or the wrong sensor air gap.
P0336 after a computer swap or reprogram, or a new crank sensor, balancer, flywheel or engine: do the crank variation (CASE) relearn.
Check or log
Watch engine RPM in a scan tool while cranking. Zero or jumping RPM means the computer isn't seeing a valid crank signal.
A noid light on an injector while cranking: no flash points at the crank signal, or power and ground at the computer.
Mismatch? A 58x-to-24x converter box exists. Nothing converts 24x to 58x: that direction means changing the reluctor.
Turn it off in the tune? No. The computer needs this signal to run right: fix the cause.
The computer doesn't see the cam signal it expects (P0340 circuit, P0341 range/performance, P0342 low, P0343 high, P0344 intermittent).
Likely on a swap (check in this order)
The cam sensor and cam gear don't match the computer's setup. Gen III reads the cam at the rear of the block under the intake; Gen IV reads it in the front cover from a 1x or 4x cam gear (the 2005–06 E40 is 24x with the front sensor).
The wrong cam reluctor behind the sensor. A Gen IV may not start at all with a bad cam signal.
Low, high or intermittent: check the connector, its feed and ground, and the signal wire back to the computer.
Check or log
Confirm which cam sensor location and cam gear the engine has, then check the computer is set up for that.
Turn it off in the tune? No. The computer needs this signal to run right: fix the cause.
The crank and cam signals don't line up the way the computer expects.
Likely on a swap (check in this order)
Cam timing off mechanically: a cam set a tooth off sets it, and a CASE relearn won't fix that.
On a Gen IV, a cam gear that doesn't match the computer's setup (1x vs 4x) gives it the wrong cam signal.
Check or log
Check the timing marks (or scope cam vs crank) before you buy sensors.
Turn it off in the tune? Never. It's an emissions code: we explain it and fix the cause, we never turn it off.
Anti-theft (VATS)
Anti-theft: no fuel enable / start enable (VATS)
P1626P1631P0633Can be turned off
The theft system didn't give the computer permission to run. P1626: fuel enable signal not received. P1631: start enable signal not correct (bad or missing password). P0633: immobilizer key not programmed (Gen IV). It starts and stalls, or won't start.
Likely on a swap (check in this order)
The donor's theft module or body module isn't in the swap and VATS is still on in the tune. That's the usual one.
0411 / P59: set VATS Control to None in the Systems tab and do a Write Entire. A calibration-only write didn't take on swapped trucks.
E38: VATS is turned off in the OS tab (Advanced view), then a Write Entire. There's also a starter-relay / starter check in the System tab that has to be off on a swap.
Once it's running, a VATS fault won't shut it off: it blocks the next start. So "it ran once" doesn't mean VATS is off.
Check or log
On an E38 that won't start, read the codes: the computer reports why it's blocking the start.
Turn it off in the tune? Yes, in a Start-up File: P1626, P1631 (0411, P59); P0633 (E38, E67). VATS off is a normal swap setting. Ask for it on the order form. Listed in your change log.
Drive by wire throttle
Electronic throttle: actuator, position and sensor agreement
P1516P2101P2135Fix the cause
The throttle didn't go where it was told, or its sensors disagree. P1516: throttle actuator control (TAC) module / throttle position performance. P2101: commanded vs actual throttle position out of range. P2135: the two throttle position signals disagree for more than 2 seconds.
Likely on a swap (check in this order)
Throttle parts from different families. The pedal, TAC sub-harness, TAC module, throttle body and computer all have to be one family or you get hard-to-find throttle faults.
Gen III: the early all-plastic TAC module only goes with the 0411; the later metal-bracket TAC only with the P59. They don't interchange.
The C5 Corvette pedal (9-pin) looks like the truck pedal but is wired differently: it only works with the early TAC module, an 0411 and the C5 sub-harness.
E40: only the 90 mm silver-blade LS2 throttle body works. The later gold-blade body looks the same and doesn't interchange.
Gen IV: mismatched electronic throttle parts can set P0606 / P1516 and shut the engine down.
Otherwise the most common cause is the TAC module or its wiring.
Check or log
Key on, engine off: throttle position reads 0 and sweeps to nearly 100% at full pedal.
P0101: the MAF reading doesn't match the airflow the computer predicts from speed density. P0102 / P0103: MAF signal frequency too low / too high.
Likely on a swap (check in this order)
On a modified engine, P0101 is often the VE and MAF tables disagreeing (predicted airflow), not a bad sensor. Swapping MAF sensors didn't cure it on a tuned engine that ran fine with the MAF off in the tune.
Running speed density with the MAF removed: the MAF is failed on purpose in the tune and these codes are set up so no light comes on. The computer needs a MAF fault to run on speed density.
The sensor unplugged or its connector damaged.
Check or log
Log MAF airflow against the predicted airflow before replacing the sensor.
Turn it off in the tune? Yes, in a Start-up File: P0101, P0102, P0103 (0411, P59, E38, E67). Only when the build runs speed density with no MAF. Listed in your change log.
P0300P0301P0302P0303P0304P0305P0306P0307P0308Emissions: never off
P0300: random or multiple-cylinder misfire. P0301–P0308: a misfire on that cylinder.
Likely on a swap (check in this order)
A bigger cam misfires at low rpm by nature, and the misfire detection can flag it.
Coil power and coil grounds, and bad grounds in general: they mimic misfires and sensor faults on swaps.
Cam timing off mechanically (often with a cam/crank correlation code).
On a swap, look at the setup and the tune before parts: plugs, wires, MAF, O2 sensors, injectors and coils all replaced didn't cure one swap's P0300.
Check or log
Spark tester on a coil, then check coil power and grounds before swapping parts.
Turn it off in the tune? Never. It's an emissions code: we explain it and fix the cause, we never turn it off.
Computer, voltage and network
Computer internal performance
P0606Fix the cause
GM calls it "control module internal performance": the computer's own self-check failed.
Likely on a swap (check in this order)
Check grounds first: bad grounds mimic computer and sensor faults.
On a Gen IV it's often set by mismatched electronic throttle parts.
Some scan tools show P060D (pedal position performance) as P0606.
Big cam or stroker combos on some E38 operating systems trip the torque-model check on tip-in (P0606 and limp mode).
Turn it off in the tune? No. The computer needs this signal to run right: fix the cause.
System voltage low / high
P0562P0563Fix the cause
P0562: system voltage stayed below about 10 V for a minute at idle. P0563: voltage too high (overcharging).
Likely on a swap (check in this order)
Alternator, battery, or the charge wire and grounds.
Swap harnesses often leave the alternator control wiring out.
Check or log
Charging voltage at idle with the lights off should be about 14.1–14.4 V.
Turn it off in the tune? No. The computer needs this signal to run right: fix the cause.
Lost communication (computer, transmission controller, body module)
U0100U0101U0140Some, on request
Modules on the network can't see each other. U0100: lost communication with the engine computer. U0101: with the transmission controller (TCM). U0140: with the body control module (BCM).
Likely on a swap (check in this order)
6L80 / T43 and other Gen IV automatics: the engine computer and TCM operating systems have to be a working pair. Use an engine OS from a vehicle that came with your transmission; a 2013 TCM didn't work with a 2007 engine computer (U0100 and P0700).
The CAN (GMLAN) wiring between them, its termination, or a connector not latched after the transmission went back in.
A standalone harness with no BCM: U0140 (and U0121, the ABS module) set because those modules aren't there.
Kept the donor's BCM? Turning VATS off doesn't break the BCM-to-engine-computer link by itself. On one supercharged 6L80 swap the TCM link only came back once the old BCM was reconnected: the other modules on the network matter.
Turn it off in the tune? U0101 and U0140 only when your swap has no TCM or no BCM, on request (E38 / E67). U0100 never: it means the engine computer itself dropped off the network.
Transmission and speed signal
Transmission controller asked for the check engine light
P0700Emissions: never off
The transmission controller set its own code and asked the engine computer to light the check engine light. Read the transmission controller's codes.
Likely on a swap (check in this order)
Whatever the TCM stored: read its codes for the real fault.
On a 6L80 swap, an engine computer and TCM from different years (incompatible programming) set U0100 with P0700.
Turn it off in the tune? Never. It's an emissions code: we explain it and fix the cause, we never turn it off.
Automatic transmission codes on a manual swap
P0711P0740P0748P0751P0756P0785Can be turned off
P0711: fluid temperature sensor range. P0740: converter clutch solenoid circuit. P0748: pressure control solenoid. P0751 / P0756: shift solenoid A / B performance. P0785: 3-2 shift solenoid circuit.
Likely on a swap (check in this order)
An 0411 or P59 still set up for an automatic, behind a manual: it sets the automatic's codes for parts that aren't there.
Codes for parts the tune expects but the harness or transmission doesn't have (a range switch missing on a standalone harness, for example).
Automatic still in the car? Then the code points at that part of the transmission (see the meanings above).
Turn it off in the tune? Yes, in a Start-up File: P0711, P0740, P0748, P0751, P0756, P0785 (0411, P59). Only when an automatic was replaced by a manual (0411 / P59). Better still, set the tune up for the manual. Listed in your change log.
Input (turbine) speed sensor
P0716P0717Fix the cause
P0716: input speed sensor range / performance. P0717: no input speed signal.
Likely on a swap (check in this order)
An older 4L60E with no input speed sensor behind a tune that expects one. That's a tune setting: the tune has to say the sensor isn't fitted.
Wiring or the sensor itself on a transmission that has one.
Turn it off in the tune? Not on our turn-off list. With no input speed sensor, the tune is set up without one (a setting, not a hidden code).
Converter clutch and slippage
P0741P1870Fix the cause
P0741: converter clutch performance or stuck off. P1870 (GM): transmission component slippage, when engine speed and vehicle speed don't match with the converter clutch applied.
Likely on a swap (check in this order)
Converter clutch or valve body wear (P1870 often comes with a hard 1-2 shift).
Compare engine speed with transmission speed while the converter clutch is commanded on.
Turn it off in the tune? No. The computer needs this signal to run right: fix the cause.
Output speed sensor no signal
P0722Fix the cause
The computer sees no output-shaft speed signal.
Likely on a swap (check in this order)
Sensor, connector or wiring at the transmission tail.
Turn it off in the tune? No. The computer needs this signal to run right: fix the cause.
Vehicle speed sensor
P0500P0502Fix the cause
P0500: vehicle speed sensor circuit. P0502: vehicle speed signal low.
Likely on a swap (check in this order)
A manual or a non-electronic automatic (T56, TH350, 700R4) with no speed sensor wired. It isn't needed to run, but without it the computer can hunt for idle or stall on hard stops.
A different sensor than the tune expects. The computer expects about 40 pulses per output-shaft turn (4L60E / 4L80E style); another sensor needs the tune changed to match.
The speed wire split or tapped for the speedometer. Never split it: a split signal can stop the transmission shifting.
E38 with a manual: the manual speed-sensor terminals only work once the E38 is programmed for a manual.
Check or log
A scan tool showing 158 mph with the car parked is the default when the computer doesn't see the speed sensor.
Turn it off in the tune? Not on our turn-off list: give the computer a speed signal.
Emissions codes
Coolant below thermostat temperature
P0128Emissions: never off
The engine didn't reach operating temperature in the time the computer expects.
Likely on a swap (check in this order)
A thermostat stuck open, or colder than stock (a 160 °F thermostat in place of the 195 °F stock one set it on a tuned car).
The coolant sensor, low coolant, or a fan running when it shouldn't (fan temperatures are tune settings).
Check or log
Log coolant temperature from a cold start. With a working stock-rated thermostat it should come up and hold.
Turn it off in the tune? Never. It's an emissions code: we explain it and fix the cause, we never turn it off.
Catalytic converter efficiency (bank 1 / bank 2)
P0420P0430Emissions: never off
The rear O2 sensor started switching like the front one: the converter isn't storing oxygen.
Likely on a swap (check in this order)
Converters failed or missing, or the rear O2 sensors reading raw exhaust.
A misfire or a bad front or rear O2 sensor.
Turn it off in the tune? Never. It's an emissions code: we explain it and fix the cause, we never turn it off.
EVAP system
P0440P0442P0446P0455P0496Emissions: never off
P0440: EVAP system fault. P0442 / P0455: small / large leak. P0446: vent control circuit. P0496: high purge flow.
Likely on a swap (check in this order)
EVAP parts left out of the swap: the computer sets codes for missing emissions equipment.
Hose connections, the canister and the purge valve; an intake leak.
Turn it off in the tune? Never. It's an emissions code: we explain it and fix the cause, we never turn it off.
Let us read it for you. Send us your HP Tuners file and a datalog. The Tune Report ($19 free while we launch) tells you what to fix first, in plain English, and which codes to expect with your build.
No tune yet? A Start-up File ($79) sets up the swap codes the right way: VATS off when you ask, MAF codes on speed density, an automatic's codes behind a manual, every change listed.
We fill in what you picked here on the order form.
Read stored and pending codes with any OBD-II reader, a phone app with an OBD-II adapter, or HP Tuners VCM Scanner. Clear them, drive, and read again: what comes back is what to chase.