Vibration Problems

[87SupraCompMN]

Hello,
I have a 1987 Supra Comp ts6m. I was having vibration problems when I ran the boat real slow or putting it into nuetral. I took the tranny out and rebuilt it...bearings, clutch plates, etc...although everything looked pretty good. We put it back in and are still having the same problem. It's aligned pretty close so I don't think thats it. I ran a dial indicator on the shaft and spun the shaft one full turn several times and it varies .010 of an inch. I would think this is a sign that its bent. The other thought would be maybe the damper but I was told those don't go bad too often. Also, if its the shaft, does anyone have the specs on the shaft as far as length goes? I know its one inch in diameter but I don't know the lenght and I would like to order one before I take it apart. Can anyone help me on this one?