Okay, I had to chase down a couple other issues I had come up first. My O2 sensor went bad, so I replaced that and it works now. My risers were leaking also and got those fixed. The studs had loosened so I replaced the gaskets (and O2 spacers) and all is well again.
Now to the noise. I casted my own bearing driver install tool out of aluminum since I did not have one before. I used a punch to install the bearing initially which I do not recommend to anyone else if you read this. I also casted some new spacers for the O2 sensor for my EMI Thunder exhaust.
I put the new tool on the alignment bar and gave it some good whacks. Did the alignment all over again. Still not smooth like butter, but as good as it is going to get. Put the drive on and still the same noise. I was pretty bummed. I am going from a MC-1 drive to a Bravo so the Bravo stuff is new to me. The propshaft was spinning and I thought that was kind of weird so I took the lower shift cable off and manually pushed it into neutral and presto! The noise is gone. Apparently my preadjustment of the shift cables was a little off and the clunking/knocking noise was the drive trying to go into the reverse gear. I have forward neutral and reverse all working now, and there is no clunking in any of them. Hopefully I did not mess up the shifting clutch mechanism at all by running it for 5 minutes and not knowing that it was trying to go into gear.
