You have two options, find a 00 EX tranny, manual ECU, shift linkage, pedal assembly, clutch cylinder, slave cylinder, clutch resevoir, few other things then pay a shop 750ish to convert.
Or....
Buy a B16A2 or B18C1 or some other OBD-2 B series motor then find a 00 EX shift linkage, pedal assembly, clutch cylinder, slave cylinder, clutch resevoir, etc. and pay the shop around 1500 to do them both at the same time. This is probably your best option.
If you want to do it yourself, (just the wiring is a pain in the ace) research, unless I'm mistaken nobody on this site has ever performed a auto-manual conversion on their own so try searching around on the internet. hybridgarage.com used to have a reference but then they stoped offering tech stuff so I dunno, there's others though.
After 2 minutes of searching I found this article.
http://www.trinituner.com/shop/manual.asp
It is for a RHD 5th gen w/ a B16A but you'll get an idea of what your getting into.