BlkonBlk97GT,
IF you want to do it, Your best bet would be to find a donor car on a JY. Talk to the guy on the JY and ask him for a total of the "to convert" parts.
IMHO, it almost makes no sense. It's a huge pain in the a$$, and you are probabely also going to have some problems with the electronics. Your ECU is set up for automatic, and so is the wiring harness.
If you really want to have a manual tranny, i think it'd be easier to sell the 2001 A/T and buy a 2000, 2001 M/T.