I'll try to clarify things.
MPowerd has a S52 M3 motor with a 1992-1995 M50 intake manifold and short ram intake filter.
Question for MPowerd : Can you rev the motor to 7000 rpm or higher? This would tell us if you have a chip or not.
For the transmission you likely have the stock E36 M3 ZF 5-speed which is came from the factory with. No need to get a Six speed as they cost 2k-3k for a used one. For the differential you could have either the 4.10:1 ratio gears that is came with from the factory with in 1988 or they may have gone with a custom E36 install of a lower gear Limited Slip Differential (3.15, 3.23, or 3.43).
As is with no evidence of cams installed in the motor you most likely have around 230 whp (wheel horse power). If you plan to go with a supercharger you can easily bump that number to 350 whp.
There are half a dozen supercharger kits for the S52 motor on the market so it would be wise to do some research or let Turner Motorsport choose one they like best with your budget and horsepower needs.
I assume you'll leave all the work to them again?? If $25,000 doesn't include the purchase price of the car you are seriously in debt in this "toy"!! If you love it and don't plan to sell it then go ahead with future mods, but if something faster and newer may tickle your fancy in the future I would say stop!! I think you'll get more enjoyment out of the car in its current state if you get into your local SCCA club and use the car on the track or autocross course.
Why have all that horsepower when your driving skills will never be able to handle it on the street. I hope your goal is not all out straight line speed and you also appreciate the capabilities of this car on a road course. How about attending some High Performance Driving School/Events?