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Yep, injector connection changed on L36's around 2000, and the ECT harness is 2 or 3 wire in random cars. Harness or sensor swap will be fine, or just grab a fresh one from RockAuto (or the junkyard).

Might want to go for the tweaking of the car's file, to keep things simple. Dunno who your "guy from Lansing" is, but I haven't been around SE Michigan since ~'06 so who knows who found some tuning habits since then.
 

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From what I see in the service manuals (finally got time to look it up)...
2-wire just has Pin A) black ground, and Pin B) yellow ECT signal
3-wire were Pin A) black ground, Pin B) yellow ECT signal, and Pin C) green signal to gauge cluster

I think this was a feature in some older OBD2 cars, before everything got on the serial data line, but various models had this randomly until ~2005 as the new canbus system became more integrated in GM's.

I'd stick with whatever sensor and wire type the car has, because only the dash (not pcm) will care if there is or isn't a 3rd wire. Swapping entire harnesses is very unnecessary and even counter-productive in some cases. If it's a 3800 car, 95% of it is already correct, and you'll have maybe 2-3 things to adapt/extend/delete as you get it routed back onto the engine. Most L36 cars I've converted to L67 (usually just via top-swap) only require removing tape for the MAP sensor location, adapting injector connectors for '00+, and possibly re-positioning the EVAP solenoid to suit the harness (boost solenoid is always deleted from the valve, with top port still connected to s/c tree & bottom port left open to air, since it's just a traction control add-on anyway... a DTC will need to be turned off).

- Dave
 

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It might be a year to year issue. Your 2004 car trying to operate a 1997.5 transmission isn't a direct swap, even though the harness plugs in. The shift controls moved inside, from the external mode switch on the shifter post that older 4t65e's have. Also, 2003+ transmissions had a completely different wiring/signal change than 1997-2002 transmissions, which I forget the details of, but maybe James can chime in.

I've run a 2002 GS transmission in my 1998 GTP and still have it on-hand, but I'll hesitate to use it in my 2004 GS unless we dig up what was required for that swap. (A.K.A. I will also benefit from the info that resurfaces about this.)
 
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