If I were to venture a guess (and I will!) It appears that there should be a 'cover' bolted on. The clip on the PTO shaft would be removed, the cover, with the seal installed and bolted on and the PTO clip reinstalled. The clip probably protects the seal from someone too progressively attaching and implement.
I doubt the bearing has moved out of position and I suspect the cover has been gone a long, long time, leaking fluid and fortunately, flushing away debris.
Though I could be wrong... again.
Look at this:
Kubota Parts Catalog Lookup. Buy Kubota Parts Online & Save!
www.messicks.com