if you really want to run a manual behind the 1JZ (or either 1JZ or 2JZ engines) and you dont wanna fork out $2,000 for the R154 or apwards of $4,000 for the V160 (6 Speed) then i suggest you get hold of a big shaft W58 from a manual MKIV (JZA80) Supra. If from a Supra then you'ls already have the bellhousing, and have easier access to the right clutch kit combination.
Might wanna try finding all your other bits from a JZA80 Supra as i THINK the drivetrain are the same sizes.. a otherwise its a custom job. custom shafts are around about $600-900 depending a few things (length, universals, yokes etc.)
Another thing to look out for are the shifter positions from the boxes. Front, middle or rear shifters.
And as Drifter4ag suggested you wont really have much driving time with a T50 behind a 1JZGTE... i think even a 1JZGE you'ld be pushing your luck