1) what does it say when you navigate into the Roms folders via command line? I’m guessing they didn’t transfer properly or are in the wrong format. I’m not clear on how you’re copying files. you don’t need to leave USB the stick in using the USB transfer method – just long enough for them to transfer
7) this is normal. you can see what games run well (and using what plugin) looking at the n64 compatibility spreadsheet on the wiki.