My shop does plenty of engine swaps, albeit v-8 stuff mostly, but the theories are the same. Physical sizes and limitations aside (will it accually fit), think of things like computer location...in some cases the computer wiring can NOT be lengthened due to possible resistance values going to the ecm (computers and milli-volts can be kind of finicky). Second order of business is sensors, and associated relays, wiring, etc...where does it all go, and how do you interface it all to an exsisting wiring harness? Do you change the entire harness or harnesses?
Personally...after all the great knowlege to be had from people on this site, I have decided that when my 3.0 is worn out...a 350 Chev is going to be installed in it's place. By the time I go through all the things I just described, for what I understand (through everyone here) the 3.0 is a junk motor...what's the point? A 350 / 350 auto (and transfer from say a 1/2 ton pickup), is a far easier swap, parts are easy to get, cheap, and the upside is more power.
Just my 2.5 cents worth, and understand my comments are generic...not specific to Toyota...just what I've done in the past.