Just got done with some required service to my '96 Outback with a 2.2L and 5-speed. New timing belt, seals, water pump, clutch, pilot bearing, and throwout bearing.

 

I removed the engine and transmission for all of this, I had a leaky transmission from a bolt that was loose on the transmission. Had a local dealership seal it back up for me.

 

My problem after getting it all back together is a vibration through the pedals when the car is in gear and the clutch is engaged. It is only felt through the clutch and brake pedals, the shifter, and faintly through the steering wheel. It is a high-frequency vibration and seems to peak around 2500RPM -- which happens to be when the engine is the loudest with its growl.

 

Any ideas on this one? I thought it might be the driveshaft, as my marking on its orientation had disappeared, so I had to guess as to which way to bolt it back up. Only the vibration disappears with the transmission in neutral, and I can feel no vibrations in the rear or driveshaft tunnel of the car.

 

My other thought was the harmonic balance/crankshaft pulley. I had to tap two of the holes on the pulley to get it off the crankshaft snout, it was welded on there. Perhaps the minute amount of material remove threw it off balance.

May be simplistic but something similar was happening on my 98 Outback Sport after the clutch was replaced. There is a spring that connects to the Clutch linkage where it passes through the firewall into the engine bay. It went from a bracket on the linkage to a mount point welded to the firewall I seem to recall. I reconnected the spring and the problem went away. May not be your problem but something easy to check.