There should not be any resistance when cycling the machine. Keep oiling, any moving metal on metal, and not just the oil points in the manual. You might have to do this multiple times and let the machine sit in between oilings.
Regarding the clicking, have you run the machine without thread (but keeping cloth between the feed dogs and the presser feet)? Or run it without a needle (and no thread), and see if it clicks. Have you changed the needle? It could be bent slightly and hitting something it shouldn't hit.
Try a new needle and tighten up the tension. Your birds nest underneath could be contributing to the noise problem.