Say I were to put a 1JZ in a 1994 W58 SC300, and instead of having to do the safety switch bypass I would ditch the auto ecu and pick up a 1JZ manual ecu for cheap from a guy close by. However, this ecu has a part number of 89661-22480, which is obviously different that any of the part numbers on the wilbo site. Are these ECU's interchangeable and PNP since they both go to a non-VVTi 1JZ with a 5 speed?

 

No they are different. You can make either one work depending on how motivated you are. You should really just pick up the motor or ecu that fits your situation best and have a wiriing harness made to match. Simple and done.