To answer a few of your questions. I rebuild TR-3550s for $175 plus parts. I think my prices are inline with about every one else's. Everything in that transmission is pretty cheap except the gears. Those gears run about $100 to $200 a piece. So if you end up having to change the gears out, then you are getting close to the price of a new transmission. It takes me about 3 hours to take one of those completely apart and put it back together. You can download the overhaul manual from TTC (Tremec is now known as Transmission Technology Corporation) for free. The overhaul manual has a blow up diagram with part numbers for every single part in the transmission. I've gone as far as ordering the case for the transmission seperately.
To make the transmission work in an SN-95, you will have to use the bellhousing that came with it. You will have to get a Fox clutch fork. The dust cover will not work either. You can leave it off, or get a fox dust cover. The starter, clutch and flywheel will work fine. TR-3550s came with a 10 spline input shaft, but it is real common to upgrade these transmissions to a 26 spline input shaft. If your transmission has a 26 spline input shaft you will have to change the clutch disk. You will have to make your own hangers for the H-pipe, or just leave them off. You will have to drill the holes in the stock cross member slightly forward, because the transmission is shorter. You will also have to get the driveshaft spacer. Steeda sells one.
Kurt