Honestly, I don't really forsee the resale value being huge on a third-gen TA with a TBI motor, with or without a stick tranny. The TPI cars will be more valuable, since that was the more performance-oriented motor. Do whatever makes you happy. Believe me, once you drive a stick car, you won't want to go back to an auto - it's that much fun. And it's easy to convert a 3rd-gen. Get everything from a V8 donor car (preferably '88-'92) and you're in business - pedals, bellhousing, hydraulics, trans, shifter, and maybe the crossmember. The 700-R4 and T5 use the same driveshaft so you won't have to worry about shortening your stock one.
For what it's worth, my '88 Monte SS came from the factory with a carbed HO 305 and 200-4R automagic. It now has a Tuned Port fuel-injected 305 from an '87 IROC and a World Class 5-speed from an '88 RS. This car is worlds better than a stock '88 SS; much more fun to drive with the 5-speed, and the torque increase from the TPI is a big bonus.
