Well,i got my fms hd clutch in today, works good..... problem is, the (whining, clicking) noise is still there

guy at the shop said it's gonna need a rebuild 425$ for a total rebuild, my tranny shifts pretty good, stays in gear? they said input shaft was fine, along with the t-o bearing, or he has a low milage t-5 out of a 93 sittin in the shop for 500$, i dont have the cash now, but i guess im gonna have to start huslin fast, i need my car, im afraid to hurt it more by driving it.
So i guess it's a gear, or bearing in the t-5, this sux, also sounds like its in the rear a little.... any opinions? thnx
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90 lx coupe: 175k miles, steeda water pump pully, hurst shifter, Mac cold air fenderwell, accel supercoil, ADS chip, aluminum D/S, Black magic fan, 3.27grs.
Best time: 13.9116(on 225/60/15 firehawks)
Best mph: 98.17
Best 60': 1.9607
next mods: subframes, mac h-pipe