Well I did a little research and talked to Matt today and figured out what was going on. The biggest problem it turns out was I did not know how the hi/low part of the spindle works. When you push the lever on the top to the back it lifts up the spline that the front pulleys are mounted on and you are only running off the back gear. When the spline disengages the clearance between the "dogs" is quite limited, so the noise I was getting was the lower part hitting the top part ever so slightly. The reason I could not get the spindle back together was that the fit is quite tight between the two shafts so gravity was not enough to let it drop into place as you rotated the pulley. Matt said to just line the "dogs" up by eye and give the ring on top a tap with a plastic hammer. The travel is only about 1/4" so they popped together no problem. I worked them up and down a few times and the friction was a lot less. In doing a little reading this is a common "problem" with this style of Bridgeport head; the set screws that travel in the cam loosen up and you don't disengage the spline totally and get what sounds like horrendous noises.
After experimenting with the speeds a bit, I am just going to leave the head in high anyways; with the VFD you get a good speed range. The range is probably just as good or better than working the pulleys and back gear.
I am embarrassed for over reacting and will be e-mailing Matt in the morning to apologize for pushing the panic button. You have to be in the right frame of mind when experimenting with things, and after working for about 11 hours I was definitely out of patience.
