Whew, That's a lot!
Not trying to make a sale.. but EVERYTHING you need to know is covered in my conversion manual... however, I'll try to answer your questions best as I can:
The TT engine fits with NO modifications into the SC300 engine bay. There is even an opening already there as provision for the intercooler pipes, and place to mount the intercooler in the right side of the forward compartment.(thanks to the Japanese Lexus Soarer with the turbo engine).
The actual year of the Supra engine used is pretty much immaterial, they are all virtually identical. It is the ECU and the wiring harness that is somewhat different with the OBDII diagnostics, and that system can be somewhat more troublesome to connect up. Best to stick with a 1995 ECU and harness, or earlier.
Also, it doesn't matter whether the engine was used originally with auto or manual, either will mate up with the stock Lexus transmissions(s).
I used the Lexus 5-speed, which is plenty strong for the job. Most sources seem to think the automatic is a bit weak to handle the extra power.
Cost? Can vary wildly... if you can get a complete Supra engine/intercooler, MAF, Oil Pump, Fuel Pump, harness, ECU, radiator, then your other costs will be less than $1,000. Obviously, any missing pieces from the Supra side will increase the overall costs.
Hope this helps!
Phil