Just a few thoughts from me.
Have you guys checked the bellhousing runout? If it is out of spec - it can cause issues. I had to buy offset dowels for my block to get it within spec.
http://www.priveye.com/images/lakewood.htm
I had a vibration in my Mustang after getting it back together. Here is the thought process I went through.
Does it vibrate when only when moving? - If so, lean towards wheel balance, driveshaft, bent axle etc.
Does it vibrate when rev'ed in neutral - this isolates it to the engine and transmission.
Does it vibrate when you have the clutch released? - this eliminates anything internal to the tranny, as it isn't spinning then. It could still be bellhousing misalignment causing wearing/pressure on the pilot bushing/bearing.
Does it vibrate with the accessory belts removed? If so, you've isolated it to the rotating assembly of the engine, which in my case is where I ended up.
My next step was to pull the transmission, clutch and pressure plate and run the engine with just the flywheel. At this point, my vibration basically went away. My findings were the (unnamed brand new) pressure plate was out of balance. Unfortunately for me - it had already damaged my main bearings
I know that was a long story, hopefully it gives you some useful information. I had driven my car less than 100 miles trying to diagnose the problem - so caution - depending on the magnitude of the vibration - it can do some serious damage.