Here is something simple to do. Go buy a $30 factory rubber trans mount and swap it with the poly trans mount you just put it. If the vibration was caused by the poly mount then it will subside. I've already encountered this issue with the poly trans mount and when I swapped it out the vibration subsided. I also already went through spending thousands at a shop to check the flywheel, new clutch, harmonic balancer and been told to rebuild the motor when what I later found it to be the trans mount. Also if you've changed the shifter to an aftermarket one you'll notice a slight increase in vibration due to loosing the factory rubber isolator between the handle and base.
If the vibration does not subside after this swap you at least know for a fact it wasn't that and you won't be out 100's of thousands of billions of dollars trying to figure out more complex factors that may or may not be the issue.