my supra gets very shaky when accelerating(only shakes after driving for about five minutes), i used to think it was the clutch slipping but the disk and pressure plates have been changed and the problem still persists. Now im thinking it is the turbo and the shaft play is too much, could that be suffocating the engine???

Where does it feel like the vibration is coming from? The rear end? The steering wheel? Engine? Also does the turbo wheel spin freely? Err.. are you trying to say the engine is lugging bad.... like having no power at all?
EDIT: just came across this post, dunno if your having any of the same problems he's got but it'll give you an idea http://www.supraforums.com/showthread.php?threadid=131515

the engine shakes really bad like it was suffocated and then all of a sudden turned on again by the fact the the car is in gear and moving. Its not just a vibration, its a sudden jerk, and when it jerks the turbo doesn't seem to be spinning, the whizzing sound stops. There may be a lost of horsepower, it jerks espeacially bad when going uphill and sudden acceleration.

the car doesn't just vibrate, it jerks really hrad when going uphill or accelrating too fast, which is a lost in hp probably. The turbo spinns freely and then all of a sudden the car jerks like the engine was suffocated and starts back up again because of the car is in gear and moving. WHne the car jerks the turbo seems to stop spinning because there is the absence of the whizzing sound.

Alright, kinda sounds like the car could be in limp mode. If you don't know how to pull engine codes, here's the site http://www.cygnusx1.net/supra/techtip/engineerrorcodes.html . Post back here with the results it gives out and i'll try and help you out.

i've done this before and according to the repair manual it says it was the code that had something to do with the air flow meter

You wouldn't happen to have a buddy with another turbo MK3 would you? Then you could just swap out the AFM's and see if that solves the problem, first try jiggling the AFM connector harness and make sure their connected good, look for obvious shorts or cuts, then try to find another AFM to swap with. Do you remember what code it threw by the way?

would the AFM make my car jerk like that? It only jerks when its really hot outside or when i've been driving for like 10mins. another thing i've noticed is that if my car starts to jerk really hard then all i have to do is turn it off for like a minute(like at a stop light) and it will run fine again for a while, which is how im driving it now. What do you think that means?

the engine code before was 31 or 32, but i just ran the dianostic again and it was just blinking continuously which suppposedly means there was no probelms. What do i DO????

i dunno what your exact problem could be but my girlfriends supra had the same problem but it turns out it was her transmission.