Take some pictures once you pull the transmission of the issue and what it looks like. Always good to see pictures.
Regarding your outer cover.... if that was my bike I would just sand it smooth and clean it up and run it. Won't see it when it's back on. Regarding the chain, clean it up and have a good look at it. If nothing looks damaged, I would run it too.
Clean up the inner primary once you have it off and all the clutch steels and frictions to make sure you get all the shavings out and no damage from the shavings to the clutch assembly.
Once you swap trans and if you reuse the parts I mentioned above if it was my project I would change the primary oil after 100 miles or so and then another time after another 500 or so. That is worth the extra $10 for 2 quarts, oil is cheap parts are not. Hell I would probably do that oil change frequency regardless if it's new parts or old parts just to check the magnet on the drain plug is clean.
I just put in a new transmission on a bike and changed the oil after 500 and again after another 800 miles. Was going to do it at 1000 but it got cold anyways and wont see that this year. Checked the magnet on the drain plug and was clean as whistle both times, 2nd oil change was obviously unnecessary but was worth the $50 for the oil just so I feel better...lol