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Should I use an aftermarket ECU or the factory computer for a budget LS swap, and how do I delete VATS cheaply?

Here is what the documentation says. Each point links to its source; details depend on your exact computer, harness and transmission.

When Passlock sees a valid R-Code in the proper timing window, the IPC sends a data-bus code to the PCM to enable the fuel system so the vehicle starts and stays running; an incorrect R-Code makes it start, run for a moment, then shut off. (Directed Electronics)
P01, P59, E38, E67: In the factory architecture the theft decision lives outside the PCM: the IPC/BCM decoder interprets the R-Code and transmits the approval to the PCM, so a swap with no BCM must have the check disabled in the PCM itself. (Directed Electronics)
Per HP Tuners, a VATS disable is required when swapping the powertrain/engine from one vehicle into another so it starts and runs properly; it is not required when tuning a stock GM vehicle. (HP Tuners)
P01, P59; LS1, LM7, LQ4, LR4, L59, LS6; 1997-2007: HP Tuners official VATS-disable procedure for Gen III PCMs (including P01/0411): in VCM Editor go to the Systems tab > Security > VATS Control and select 'None', save the file, then perform a Write Entire (not a calibration-only write). (HP Tuners)
P01, P59; 1997-2007: VCM Suite Online Help defines the Gen III VATS Control types as: Serial = Class 2 VATS, PWM = PWM VATS, None = VATS system is non-existent or disabled; VATS Fuel Cut determines whether fuel is cut when VATS fails. (HP Tuners)
P01, P59, E38, E67: Per HP Tuners' owner, setting VATS to disable in the PCM stops the PCM from cutting fuel when the VATS signal fails, but it does not disable the vehicle's security system itself (e.g., BCM-controlled crank interlocks remain). (HP Tuners)
P12; V6 (LSJ-adjacent): On an older GM V6 P12-type PCM, the documented workaround was to set the VATS value to PWM and set VATS DTCs P1626 and P1629 to '3 - No Error Reported'. (HP Tuners)
E67; LSA, LS9; 6L80E/6L90E; 2009-2015: PSI states that all of its standalone harnesses (e.g., HAR-1098 for 2009-2015 LSA/LS9 with 6L80E/6L90E and E67 ECM) require PCM VATS removal, which PSI offers. (PSI Conversion)
P59; LM7; 1999-2006: MotorTrend's DIY LS swap wiring guide (based on a 2002 Tahoe 5.3 harness) separates physical harness simplification from PCM reprogramming, and says the PCM must be reprogrammed to remove VATS. (MotorTrend)

Confirm against the instructions for your exact parts before wiring. More: VATS / anti-theft in our tuning guide.

What we recommend

We recommend keeping the factory computer. An aftermarket ECU costs $1000+ and needs a full tune just to get about 95% right. An HP Tuners suite (~$700) lets you turn off VATS and the other swap-blocking settings and then drive the car. A free option also works: TunerPro plus a cheap Bluetooth OBD2 dongle with LS-Droid can delete VATS, enable PE and control e-fans. Adding a cam later to an engine that already runs is easy to tune, because only the VE table changes and the MAF table doesn't. We also don't recommend a V-belt setup on an LS swap, because the belts slip, rob power and can come off at high RPM.

Check this first:

That your tuning tool and cable support your specific PCM
Save a copy of the stock file before writing any changes

Based on what we've seen work across our own builds, our friends' builds and the wider LS community, reviewed by our lead tuner (20 years of LS tuning). Every combination is different, so use at your own risk and check our safe tuning limits before any wide-open pass.

Should I use an aftermarket ECU or the factory computer for a budget LS swap, and how do I delete VATS cheaply?

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