Ok, correction. I was thinking automatic transmission when I said flex plate. Disregard what I said. The cover being off is not good because it allows debris to get up in there. Check the starter drive gear though. Just reach up and see if it will slide all by itself. It should not. I think you could have a throw out bearing making noise though or the pressure plate springs or the clutch disc springs. Sorry about the misinformation about the flex plate. I have never seen the flywheel crack where the attaching bolts are. You do not have a flex plate.