I had energy suspension poly mounts in all three spots. I later swapped the trans mount out for a rubber OE mount. It reduced the vibration in the shifter slightly to a more confortable level.
But with all three, i never had an all-car type of vibration. It was more just in the shifter handle that annoyed me.
Have you made sure that no parts of the exhaust system (including headers) are not touching anything they shouldn’t be? What about the exhaust hangers? Are they in good shape including and rubber isolation parts as needed?
If the vibration is related to engine RPM and completely independent of vehicle speed, that sounds to me like a harmonic balancer problem. I did notice more vibration when I upgraded all my mounts, but it only happens around at high speeds, which I'm fairly certain is because the stock driveshaft is not perfectly balanced. (From what I understand that is a pretty common problem.)