Yes, ALOT of differences. Just in the soarer alone that I know, and theres more:
There are 6 engine harnesses out
91-94 auto/manual
94-96 a/m
97-200 a/m
Then you also have Generation Differences in Soarers.
Gen 1 = 91
Gen 2 = 92-96
Gen 3 = 97-2000
Now, what about all the other cars?
The Supra and Gen 1-2 Soarer share nothing electrically except some sensors and the given stuff like coil packs.
The cooling systems are different. Transmissions different. Downpipe/exhaust different. Different throttle body.
What do the Chaser and Soarer share? Mostly everything except oil pans. Harness has differences but ECU's are direct plug and play between eachother.
Chaser and Supra? Please read Supra and Soarer.
What about the VVTI from 1997 to 2006? Not alot of information is out there for these cute motors. The basics still apply.. don't expect to plug in a Verossa motor in a Soarer or Mark II Bilt.
Sorry, but the Supra only got to Gen 1, no VVTI without some major work.
Please note:
Backwards compatibilty is insane. You want to install a 1994 Soarer motor in your Supra? Sure, simply unbolt all the soarer specific things, and bolt on your 1jz Supra specific things.
Want a Verossa 1JZ-GTE VVTi in your 1991 Supra? Not an issue, just swap things out. The only thing you won't have is VVTI due to 1991 ECU not having that in it's program or harness.
What about a 2JZGTE in your 1JZGTE Soarer? Easier the pie, you'll just need a SAFC2 to control the larger injectors on the 1JZGTE ecu.