83GTMUSTANG: Might wanna turn off the caps lock key, dude. Punctuation would also make your posts easier to read.
As for the hard running when cold, there are a couple of things to check. First on my list (because I'm a geek) would be the coolant temperature sensor. That's the one in the steel lines going to and coming from the heater core, up on top of the engine. My reasoning is that it's possible that the sensor isn't sending the correct information about the actual temperature of the engine, thus it's not adjusting the a/f ratio for the operating conditions. Also, after a certain amount of time has elapsed, the EEC will look at the oxygen sensors for feedback to know where the a/f ratio is (within certain limits). Is the engine full of coolant, even when cold? Was the sensor wiring damaged (done this one before!)? How about the last time it was replaced? If you could take a measurement of the resistance across the terminals of the sensor when cold, and then when at operating temperature, it might reveal something.
The other more-likely problem I would check is for possible vacuum leaks. Anywhere from the throttle body down to the intake valve is a candidate...but since it appears that the heads you are running are shaved, I would be led to believe there could be some gap between the intake manifold and cylinder head. It's entirely possible that the gap is there when the engine is cold, and is eliminated when warm. Thermal expansion is a b!tch. Read your spark plugs if it's being a bastard to find....even if not it could be another clue.
Only other things I could think of are air being drawn into the exhaust stream, or a lean condition until the engine is in closed loop (cause to be determined).
Regarding the vibration, your driveshaft shouldn't move at all from the axis of the tailshaft, only along it (in statics, I would say only translation along and rotation about the z-axis, if the tailshaft is the z-axis). Replace that bushing and seal!
Good luck.