Nice work!
Honestly i think bobcat will charge too much for an O ring, i would have just used high temperature silicone or Loctite 515. See what Bobcat want for the O ring, if too much i would just go the silicone way. Even standard silicone woild do the job. This is how i re-attached my gearboxes back to my chain case, it was a saturday afternoon and i wanted them back on so out came a tube of red silicone.
The small scores you see shouldn't cause too much of a problem, they have it all worked out. As the motor wears you get a bit more leakage which your charge pressure compensates for. Hopefully that is all that was wrong! then you will be an expert in hydrostatic motor repair