you should do the tranny swap and motor swap all at once. unless you can find one of those rare B16 auto trannys (almost impossible).
to do the tranny swap you'll need this:
tranny (of course)
clutch
flywheel
clutch pedal assembly
brake pedal
lines
shift linkage
shifter
slave cylinder
tranny mount
new guage cluster (if you want)
ECU for a manual
and the rest i can't remember so i will post more if i remember. and most shops don't want to do it, but if they will usually it will cost you about $1200 labor only.
Becca