First question would be what are you swapping from? I'm assuming an NA.... so here it goes....
1. 2nd gen is 225hp.... 3rd gen is 245hp. 3rd gen has a different turbo, no afm.... pretty sure most of, if not all of the internals are different. If you are shooting for high power.... there is no great advantage in either one. Pretty sure all 3rd gen's have an LSD also.
2. 3rd gen clip is ~$3,500.
3.
http://mr2warehouse.com
4. Dunno
5. Yep
6. As long as its not the 3rd gen.... yes.
7. Same as above.... excluding the turbo.... they have ceramic turbines.
8. If you get a complete wiring harness from the kick panel back.... you should be fine.
9. Make sure you get the intercooler, afm (if 2nd gen), intake piping, intercooler, bov, ecu, fuel pump (different from NA), coil and ignitor.... a lot of things that sit around the outside of the engine show up missing a lot.