If you do it correctly, there is no difference in how it will drive, and i dont see why it should effect resale. As long as the inhibitor is looped so the car always thinks its in N (as far as the engine is concerned) it will run fine. I had been running around on the standard diff/ auto ECU for ages till i changed to a IMPUL ecu, and it went fine, my gearing actually worked out slightly taller than a factory manual, so im thinking it must at least have a 4.1 in there..
Auto ECU runs slightly more advanced timing, so you need to be careful with boost, but 9/10 a manual conversion car will be faster than a factory 5spd due to the diff and ECU. This is the case with 32's anyway.