they could have some crap on them ,so yep a cleaning wouldn't hurt .while you have the pads off ,give the wheels a spin just in case you are getting a bad bearing.
as far as your other question goes,did you get in a bad stuck or get it hot, it does sound like your cover is a lil warped, but you could double check the cover bolts to make sure they are tight . you can heat them back up an straighten them out but it is tedious. you need to find out why it got warped in the first place ,in case you have a mechanical problem ,just so's it doesn't happen again. not likely, but take cover off and check to see if the main clutch bolts are tight
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