could you possibly have gotten some debris from the clutch explosion in there and it ruined the seal? Do you have pics of the sealing surface of the seal that you can post up? Have you compare the I.D. of the leaking seal with a new (uninstalled)seal to see if it is out of spec.......could excessive heat have caused the seal to fail prematurely???
The seal is what I am thinking.......it is the most likely culprit. There are lots of Mavericks that have the same issue with the front differential seals but most people would never know about it because it is not something you would normally look for unless it leaked enough to drip on the floor..........
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?