I think you should put in the 3FE, but keep the manual transmission. Since I have a 3FE in my garage ready to swap into my 40 someday, I would love to be able to go to school on you! Besides, 20 more HP than a 2F, fuel injection, better balanced from the factory with the ability to rev considerable higher...nice swap. And you are dealing with similar HP and torque rather that doubling it like you would with a V8. AND it is still Toyota! Do it!
Sascha Steinway TLCA # 20217
1977 FJ40 "Ripper" (because it shreads!)
1988 FJ62 "Dino" OME, now in the hands of my daughter
2013 F-150 "Black Ops"