Rpm related vibration 5.9 magnum

I Can only come up with three things. Get a mechanical advance distributor and lock it to see what happens. A digital 6 has a 20 degree retard built in for start up for running a locked distributor so just set the timing at 34 for a test. you can always unlock the distributor and set it for 15 initial at Idle if you would like.

Second is the balance of the motor seams like the culprit. I had a crate motor that took a neutral balance converter . It was installed with a converter with weights and it vibrated.

Third Are you using a flex plate for a externally balanced motor and still adding the weights.

From my experience in what you are describing you have a balance issue. Unless you have had it balanced yourself you can never trust the parts you are applying. You need to take it to someone that has parts they can through at it with no cost for testing. Other than that you are just going to ruin the motor. It won't take long to destroy the bearings in that motor. especially the thrust bearing.