Ok, so I am guessing we have ruled out the improper shaft length.
On a good note, I went back at it today. It took me roughly 20 minutes, by myself, climbing in and out after each turn, but I got the motor aligned perfectly. I kind of strayed away from the whacking all 4 sides of the bar at first and just used some good old fashion elbow grease and leverage and tried to move the bearing angle specific to where I "thought" it should be. I did this about 3 times before it felt right and started adjusting the motor. Got it nice and smooth, then bumped the starter. I colored one of the bolts on the pulley so I could keep track of the crank position. First 90deg and it was a little stiff but I was able to adjust it out. Checked at the rest of the cardinal headings and it was smooth throughout with even grease marks. I tightened everything up (including checking the aft mounts before I started) and then rechecked the alignment. Fought a little to get the drive back on but it was because I was by myself, and the splines were off a bit and I played hell trying to turn the shaft without the prop on it. Once I was able to twist it a little bit, the drive slipped on. Tomorrow I will fire it up and pray to the boat Gods that my rattle is gone.
More to follow tomorrow.