1988 Chevy Nova

I recently had a auto repair shop replace the transmission in my 1988 chevy nova ( Toyota Corolla) with a used one from an auto salvage. The prior trans would not stay in 4th gear. But with 282,000 miles what can one expect. While they were replacing the trans I had them install a new clutch, flex plate and throw out bearing. Two days after I dropped it off for repairs the auto shop called and said I needed to replace the flywheel because numerous teeth had been damaged which I already suspected because the starter not always engaging, so I agreed. When I picked up the 1988 chevy nova I noticed immediately when cranking over the engine something seemed out of balance. When the car started a vibration that was never there before was very noticeable. What would be the most common problem? The flywheel may be used, could it be out of balance? The vibration occurs with 5 speed trans in neutral as well as in gear moving forward. Are there alignment (balance) requirements for the trans shaft into clutch/ flex plate? Flex plate (new) out of balance? Flywheel not torqued right, not aligned correctly on crank shaft. No problems with the used trans, works great otherwise. I'm sure the vibration will damage something if left uncorrected. Thank you for your help in advance. Ray