Personally, I would do as you suggested and remove the oil pump and plastic gear on the inside of the clutch housing. You can either remove gear and leave pump in place or remove all together and make a block off plate.
You might get lucky with the trans if you run it through a few heat cycles with a couple fresh fluid changes, but chances are you're going to have to split the cases and inspect. I would look for bent or worn shift forks, cam followers, ect. Discoloration and galling shouldn't be present. Make sure everything moves smoothly. Also don't be intimidated by splitting the cases... Its very simple once you open it up. Just lay the motor on its magneto side and pull the top half off. The trans internals will stay in the lower part of the case. Now would be a good time to do crank seals. Also if your rod is loose it would be a good time to do crank bearings and a new rod kit as well.
Hope this help, and let me know if you have any other questions.
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82 YT175
PK Racing Pipe
DT175 Jug
82 YT175
DG Head
Bassani Pipe
Rear suspension
YZ80 Forks