Originally Posted by CSkipR
How do you check the rotor to see if it is cocked. Do I take the shaft seal apart? I'm sure the rotor is the correct size since the other side is fine.
The rotor is the stainless steel part that is fastened to the shaft with set screws. Secure your dial indicator on some part of the hull and zero it out on the outer rim of the rotor and turn the shaft by hand. That will give you a radial runout and show if the shaft is bent or the rotor is not centered on the shaft.
If it does show a large displacement, zero the indicator on the shaft just forward of the rotor and see if it indicates the same displacement. If it does, your shaft is bent, if it does not your rotor is incorrectly aligned.
If the indicator shows no problems above, zero the indicator on the front face of the rotor and turn the shaft by hand. That will show you if the rotor is sitting at an angle to the shaft centerline, i.e. if it is cocked or displaced axially. This is most likely the cause of a wobble if the shaft is not bent or out of alignment. There are several reasons the rotor could be displaced, too large a bore, junk between the rotor and shaft when it was installed, bore not 90 degrees to face ... that's why manufacturers hire QC techs.
In any event, make sure you let us know what you find. I am sure you aren't the first or only person to see this and your findings add to the database here. Good luck, hope it is something simple.