So, you're saying it vibrates in or out of gear, either while moving or while at a standstill, and the vibration coincides with RPM's, correct? That pretty much rules out anything from the tranny on back, then, so at least you've narrowed it down to something with the motor. I still doubt that it's the crank, itself, though.
Even though you replaced the balancer before, have you looked at it to see if it's still wobbling? It's possible that you got a defective one, or that it may have been installed incorrectly/damaged during install (it happens).
Only other thing I can think of is, being that it's a 5-speed, is that your flywheel may be out of balance somehow. Either one of the tack-welded weights might've come off somehow, or it may not have been properly torqued down if/when it was last serviced, and so it's wobbling like mad. Do you have any vibration in the clutch pedal?