Few questions.
 

I have a 90mustang GT 5spd and everytime I come to a stop or slow down I hear a whinning sound coming from under the car like it kinda sounds like i have a supercharger its werid I really dont notice a difference in driving, just that when i put it into 5th I get a bit of a grinding and some resistance and the same sometimes with reverse.

so does it still whine when you are at a stand still or only when you are slowing down but still moving?

the t-5 can whine a bit, I notice it on my car when I'm in third with foot off the gas coasting. Also if you have an aftermarket shifter without that rubber Bullsh*t like the stock one you will hear more noises from the tranny

If it whines even at a stand still could be the fuel pump. They tend to whine when they get older.

let us know a little more

its like when i'm coming to a stop or just lettin off the gas when the car quiets down it sounds like a quick little high pitched whining noise.

Do you have ABS? My ABS controller on my 95 makes a whining noise when I hand-turn the wheel and the car is off. I dont know about yours but my ABS controller is located on the pass side of the radiator. It has little valves and motors in it. Maybe it's not functioning right on yours. Probably far fetched but it's worth a check.

its probably your throwout bearing, i just put a brand new one in mine and its whining already(quality ford racing parts) if it goes away when you push the clutch in, its most likely your throwout bearing.