I would say if it does end up being the trans for whatever reason then if you have the money I would go with the rebuilt trans since apparently you like how your truck trans was rebuilt and it sounds like your manual trans swap is a long ways from happening.
You could buy the used one and it could last a year or 91 days and at that point you will have already paid for a rebuilt trans which being a th350 it will probably last the life of the car if rebuilt right.
Very good point. The price of the rebuild is $175 more and my transmission guy is pretty damn good. The TH350 he built for my truck works flawlessly, shifts quick and firm and the time from drop off to pick up was quick. It would probably make more sense to have him rebuild it.