So to summarize:
Mechanic replaced 3 speed manual with t5 and then had extreme rhythmic vibration no matter which gear or clutch engaged or disengaged
Another mechanic took t5 out and bench tested, said tranny was fine
First mechanic took t5 out again with bellhousing, pressure plate, clutch disc, etc.. still on and ran motor, no vibration said smooth as silk
Put t5 back in, vibration still there
Took driveshaft out and ran with yoke in to keep oil in, still vibration
Next step
loosen tranny mount and jack tranny up SLIGHTLY to see if any difference? May have to widen shifter hole in floorboard
Check again to make sure tranny not touching anything
Take stick of dynamite and blow whole thing up(just kidding, maybe)