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i was talking to phil via Email and he says that the 2jzgte will bolt right onto the stock SC 5spd tranny. In terms of the gear box, i think fred is right... it may not hold up to more than 350 hp.
I've put some 30k miles on my stock SC300 5-speed manual, all the while pushing near 450 HP from my modified 2JZ-GTE... the transmission has a total of 170k miles, and is quiet as a whisper. Of course, if you're the kinda guy to rev it up to 5 grand and drop the clutch, then, naturally something is gonna break.... treat your equipment with respect, and it will last a long time!
A lot of you guys are smoking crack. You're going with 1JZ because it's cheaper. Guess what. If you're not willing to shell out a little more money for the 2JZ, then don't do it. Overall swap will be pretty expansive. If you want less power go ahead and go with 1JZ. Also keep in mind if something brakes (and most likely will if you plan on further modding the car) you will pay the premium price for all the 1JZ parts. Stop thinking in short term and expand your thinking.