is it a bitch to put a auto transmission in a yota that came with a 5 speed?

depends on wether you have a donor vehicle to get all the neccessary parts from.

ecu if the motor is fuel injected
radiator (cooling for the tranny)
cooling lines
gear selector (cables to boot)
flexplate
starter
wiring harness

I'm sure there is something else I missed but i'm not really sure what else is needed for the toy swap.