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i took my tranny out with the GE when i did the swap, i was reusing my 5spd tranny, either way, take it out, i cant imagine how long it would have taken to tighten those tranny bolts with it already in the car.
Well, you should use the 1jz tranny assuming you do not have a stock 5 spd in your SC... I heard the stock SC autos suck.. But if you were to use the 1jz tranny i'd get it rebuilt thats just me tho.. I wouldn't trust that tranny, could have something matter with it. So just tear it apart and look at it..or take it to a shop