Not worth it, in my opinion. There are plenty of manual MR2's out there. Keep looking. You'll find one.
It's a lot of work to convert auto to manual, even if you are doing a swap. The only thing doing a complete swap is gonna save you is that you'll already have the manual tranny. You'll still have to collect a butt-load of parts from a manual to install in your auto. (ie. pedals, shift linkage, clutch master cylinder, etc. etc. just to name a few).
If you already had the car, and just wanted it to be manual, then I might say go for it. But you're still searching for a car. Save yourself the headache and keep searching for a manual. You'll find one if you look hard enough!
Good luck!