Do a quick stroke check to see if it is a 3.784 or 3.984". I have a sneaky suspicion that the flexplate does not match the crankshaft. I had a '69 R Code mustang that I bought with 4 speed, and it had the N heads, CJ cast iron intake, carb., exhaust manifolds, flywheel, four speed, etc., etc., and on the drive home it vibrated above 2000 rpm and just got worse the faster I drove. Upon teardown, it was a 390 flywheel. Looked perfect, looked correct, until you turn it over and see the weighted side was smooth. The other scenario with imbalance(different car) that I experienced was a piston stuck and when I tried to start the CJ after it had sat for over a year, it would not turn over. I thought it was just a weak battery, so I put a new battery in, and jumper cables to a running vehicle with the new battery. It moved an inch or so, and then popped, and started running. I drove the car for three years with a miss and vibration. No amount of tuning would get that miss to go away. When it finally broke, on teardown, there was a rod broken in three places. The small end was still attached to the piston stuck almost at TDC, and the big end was still spinning on the crankshaft. Had oil pressure, and felt strong, but vibrated. I really have had three CJs that gave me problems since they first came out in 1968. I like FEs, but the CJs have bit me several times. Joe-JDC