Got me thinking now that we got some info. So reving past 3k in neutral the motor shakes. So I think it is safe to say the it won't be wheel out of balance. Safe also to say that it is not the driveshaft. Since your not moving the driveshaft is not moving also.
You changed the Balancer, Flywheel, ? Did you change the balancer and flywheel yourself. Or did a shop do it. Where they New parts or used parts also? It is possiable that one of those 2 parts has the wrong counter weight. There are 2 weights a 50oz, and 28oz. If one end has a 50oz and the other end has a 28 oz. That will make an issue. A stock motor I think is 50oz on both end's
Now if both are correct OZ's Then let's look at the motor. You have the crank and rods that rotate. Pistons run up and down. You have the cam which roates in the middle of motor. Then you have all the push rods, lifters, and rocker arms, These are the only parts that rotate or move up and down that could affect rpms if they are wrapped and will make the motor shake.