Your problem is exactly the same as one I am trying to solve right now. One of the best driveline guys in Denver is walking me through some steps trying to solve and I will pass them on to you. His first step was to check the bolts holding the pressure plate. This may not apply to your motor. Maybe a shop like Ground UP or Ricks can tell you if there are specific bolts to position your pressure plate to the fly wheel. I could check mine through the inspection plate and by replacing these bolts, the vibration was reduced by at least 50% (but still there). Next step was to pull the balancer on the front of the engine and check it for cracking and to see if the outer ring may have slipped in relation to the inner ring. To check for slippage, bring the #1 cylinder up to TDC and make sure that the timing pointer is aimed at "0" on the balancer. If not, something is off. Next, even though you said the motor mounts are new, I would put on the e-brake, chalk the tires and with the motor running pop the clutch a bit and see if the motor lifts from the mounts. Someone can assist you with watching the motor but make sure they are standing to the side of the car in the event it jumps forward. Now if all this checks out, it's time to get under the car and pull the tranny. Take the flywheel, clutch and pressure plate in to a shop that can inspect and balance for you if needed. They should be able to tell you if you have the correct fly wheel. While you have the tranny out, check the pilot bearing and see if it may be worn. My flywheel is getting balanced right now so we will see if that solves the problem. If not, he said there is a problem in the engine - at which time I cry and throw things. I hope someone else will add to this if there are other things to check, but that is the process I have been though. By the way, just sitting, my car has no vibration until about 2,000 rpm and then vibration starts and gets worse up to just over 3,000 rpm and then it goes away completely. Best wishes and I hope you will let us know what solves the problem.