I Need Help With My Mustang??

I need help I bought a 96 ford mustang 3.8l manual trans, is this what they call sn95? I also need help very bad when I bought this car I was told that it had a replaced motor 3.8l from a 97 but that was it besides that the heads needed shaving. well I now have over 2000.00 in it and trans mission on first drive wore out output shaft rear seal bushing and yoke spline. I replaced it. now I don't want to drive it because since I bought it and fixed it, the whole car shakes from motor, steering wheel, seats doors hand shifter etc.. I believed this might have been what caused the trans to mess up bushing and seal and yoke. the timing is good harmonic balancer goo trans and motor mounts good etc.. I keep going on. any way called the kid back and now he tells me that he put the motor in from a 97 automatic 3.8l. and have not gotten any flex plate eight with it. I believe this shakes coming from motor not balanced now with the manual ??? was told to have one machined ??? does anyone no if this is it?? is there actually a fix. do I have to have my flywheel machined to the specs of a 97 automatic 3.8l flex plate if I get another one. will this work or is there any place that sells what I need like new flywheel with correct balances for this mess? please help if u know for sure i am right

I also heard or seen in a youtube posting that the eom yoke on the manual with that balancer weight , I seen someone saying that once you replace it that you should go with the like 5" long slip yoke because the oem one is 6" into the trans and that its not good to have. that its to long and goes to far into the trans? is that why I could not find the same one aftermarket? is that why my trans output bushing and seal and yoke wore out too? or is this from the motor shaking so bad or both ?

yes this motors been like that since the kid put the wrong year and automatic car motor in it! and I put all new parts in , plus he said its been doing this since he tried starting this motor but never did this with the old one. plus there are many tyes of motors like these that have different balances