sorry....didn't read far enough down to see the whole story. I don't want to scare you but checking run out with the clutch off and not under load may not tell you the whole story. If the PTO crank bearing is out of tolerance, you may not notice it when doing a static test without any load on the crankshaft. But when the machine is under a load, the crankshaft could be flexing from all of the force put on it if the bearing is not in spec......You should be able to get an indication of this by looking at the inner race of the seal. It would look worn and would be out of spec when compared to a new seal.
Here is a long shot....have you checked your oil level to make sure you are not overfull or do you park it for extended periods with it in a position other than relatively parallel to the ground?