How do I defeat or bypass the third-gen VATS/Pass-Key system during an LS swap (keeping or removing the stock ECM)?

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

• VATS (Vehicle Anti-Theft System) is GM's umbrella term for its factory anti-theft families: PASS-Key I/II/III (key-based systems) and Passlock (lock-cylinder sensor systems), all of which gate engine start/running through the PCM. (General Motors (via NHTSA / govinfo.gov))
• pre-1997: The original PASS-Key system is passively activated (no operator action beyond removing the key) and consists of an ignition key, an ignition lock cylinder, and a decoder module. (General Motors (via NHTSA / govinfo.gov))
• 1997+: PASS-Key III uses a transponder embedded in the key head energized by a coil around the lock cylinder, with over four trillion possible unique key codes. (General Motors (via NHTSA / govinfo.gov))
• 1997+: In PASS-Key III, a valid key makes the decoder send an encoded message to the PCM enabling fuel flow and starter operation; an invalid key makes it send a different password that disables both fuel and starter. (General Motors (via NHTSA / govinfo.gov))
• 1997+: PASS-Key III cannot be defeated by removing and reapplying vehicle power, and replacing the decoder module will not defeat it because of its decoder module password. (General Motors (via NHTSA / govinfo.gov))
• 1997+: PASS-Key III performs a five-second security-light bulb check at key-on, which goes off for a valid key; an invalid key turns the security light on, and a fault detected during normal operation also enables the light. (General Motors (via NHTSA / govinfo.gov))
• Passlock I and II are key-based, fuel-shutdown anti-theft systems requiring the key cylinder to be mechanically turned with a key: the Passlock I R-Code goes to the instrument panel cluster (IPC), while Passlock II sends it directly to the BCM, which houses the decoder. (Directed Electronics)
• Per Cardone, the Passlock lock cylinder contains a stationary Hall-effect sensor and a rotating magnet; turning the key creates a coded signal sent to the IPC or BCM, which then messages the PCM over serial data that the vehicle may be started. (Cardone ProTech)
• A fuel-enable bypass module only enables the fuel injectors; it does not defeat the starter interrupt, so the crank-disable relay must also be bypassed (jumper or rewiring), and the security light may stay on. (timers.shop)

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