I would suspect the clutch disc, or the engine; the giveaway for me is that the vibration changes with engine rpm. I have had the discs spit springs out on me and or crack the hub retainer plates, or both, or just cast off friction material, all of which caused vibration.
You can sorta prove this by:
A) putting the trans in gear, depressing the pedal, then reving up the engine, with the car not moving, into the usual vibration zone; and then not having any vibration. This proves it's not in the engine or clutch. The disc however was stationary, being anchored by the in-gear trans and driveshaft.
B) Next, you put the trans into neutral, do not declutch, and again rev it up. Now the disc is rotating with the engine, and spinning everything inside the trans that is not integral with the mainshaft.Namely the input, the cluster and the 3 gears on the mainshaft; But not the synchronizers. Vibration now would most likely be the disc.
C) but if no vibration thus discovered, it would have to be after the trans; or remotely, something in the synchronizers or Mainshaft, which is not likely; possible yes, but not likely. You can prove this too. Drive the car up to the vibration zone in direct gear. Leave it in gear, declutch, and shut the engine off. Then a second or two later kick it into neutral, and let the pedal up. Note any vibration difference;Any vibration remaining would almost have to be after the trans.
Alternatively my CFII, has vibrated occasionally, since new. The flyweights seem to have something to do with it. Sometimes, once at cruising speed, I have to declutch and blip the throttle several times, before the vibration is minimized.