I have a 91 4Runner that is in great condition, but I believe that I have thrown a rod. (Clunking noise that sounds like a jack hammer, under powered, yet still runs smoothly). Any tips on what I should look for in a mechanic for an engine replacement? How much should I expect to spend? What engine parts do you think i will need to replace (block, piston set, what else?) Thanks

Check this out:
http://www.yotatech.com/forumdisplay.php?daysprune=&f=2
There's a lot of guys who have done a swap or need engine work. It is a lot of reading and searching!