Need to find a JX90/JZX100 R154 box as they have the remote shifter setups. JZA style manual boxes wont fit. You will need the pedal box for the floor, clutch master cylinder, clutch slave cylinder, clutch line, clutch itself, flywheel, pressure plate, change the spigot bush bearing in the back of the engine, tailshaft, manual surround for the centre console, can run the auto ECU on a manual conversion if funds are tight, you also need to work around the electrical issue with the ECU thinking the car is in park and not starting, Dont need to change the radiator but would need to block the auto tranny lines, dash cluster change if you dont want to look at the gear selections, etc etc.
Easy enough to get around the traction control and "snow mode" if you do some research there is a JZX90/JZX100 forum here in Aus with plenty of info:
http://www.jzx100.com/forum/Pity they didn't release many of the JZX90/JZX100's in manual form, less than 10% of each model were released as manuals and are highly sort after.