First, all things being equal I'd stick with the 350. Second, do you know what gears you have in both rears? Is there something wrong with the trans am rear that would make you think the 86 would be a better choice. I assume you've measured and both will fit. I would leave the rear alone unless the 86 has disc brakes. I know the 2002 rear disc brakes will bolt on to the 80s rears but not sure about the 86 to 2000.
You didn't say anything about your front suspension. The price is right, you could sell the 86 rear for 50.00+ and the whole thing for scrap metal for more than 200.00. You would have to measure the gas tank to see if it would fit. I would avoid the fuel injection route, it's a lot harder job setting up than the carb.
