I am looking a purchasing a clean 87 22R powered 4runner with an auto trans. How difficult would it be to swap out to a manual trans

 

Welcome to yotatech! It depends a lot on your mechanical ability and the tools that you have available to you. For tools you need a transmission Jack, or at the least a good floor Jack, ( I don't own a trans Jack so I usually use a floor Jack and ratchet straps)
The easiest way to get the parts you need would be to get them all off the same donor vehicle. Parts you'll need are: of coarse, manuel tranny, flywheel ( id advise getting a new clutch assembly, pressure plate throwout bearing, pilot bearing and having the flywheel turned) youll need a clutch pedal/brake pedal assembly, and a master and slave cylinder with the hard hydrolic lines. I could be forgetting something. I'm pretty sure you'll have to cut a hole in the floor for the trans and tcase shifters ( maybe make a template from the donor vehicle?) and you might have to cut a hole in the firewall for the master cylinder. That's all I can think of, I could be forgetting something, but I'm sure someone else will chime in, or If you have time check out Bill's (RMP 8080's 1989 4RUNNER RESURECTION BUILDUP) he is in the middle of doing this swap on his build thread. I hope you buy/enjoy your new 4 runner, Good luck with the swap!