mix match or find a new tranny

I have been trying to keep the same motor and transmission together in this 1966 mustang looks like the motor got changed out and the fly wheel is set up for a 10" clutch. the transmission is a three speed with the 8.5 inch clutch. I mixed the clutch kits Napa sold me and got the car on the road running reasonable well. I busted gears in the transmission . I did some checking around and the heavy duty 3 speed is hard to find I decided to rebuild the one I had. The rebuilt one had vibration apparently the inside of the pilot bushing was to big for the input shaft I put in the transmission. the inside diameter of the throw out bearing is also sloppy on the shaft but id rather have that the the out side being too small for the clutch fingers.???