Well if you are running an aftermarket shifter that does away with the rubber bushings. Plus you are running stiffer crossmember bushings and polyurthane motor mounts an a rubber trans mount you will have more vibration in the shifter. If every bushing/mount were stock you wouldn't feel any vibration..because the rubber does a great job to insulate. But the stiffer performance stuff last longer and it keeps stuff more in place but it does not the insulate that well so you get more noise/vibration . So long story short performance comes with a price and sometimes it's comfort.
after my experience,sounds like a unbalanced flywheel or flex plate....just a thought though
What you're describing sounds more like a harmonic imbalance. If you end up taking it apart again to have something checked, just be sure to clock that piece in an orientation that is different from where it currently sits.
It's your call..but i would have just changed the trans mount to match the motor mounts and see if it cut back on the vibration. Think about it everything else is stiff and you have that one rubber mount for the trans so when the vibration comes were do you think it goes..to the weakest/softest link the rubber trans mount.