Okay, my AR now has damage to the fwd lip in the radiused area of the ejection port, and I cannot close the cover. Is it okay to just file it down, or should I replace the upper reciever?
I'm not sure why it is jamming either. It seems that the bolt is cycling too fast for the brass to clear the port before it moves fwd.
It doesn't happen alot, but it has happened enough to damage the lip of the ejection port.

Take it to a gunsmith who is competent with AR style rifles and let him diagnois the problem.  I'm curious, what kind of AR?  Is it a factory built gun or a kit or aftermarket clone?  Does it have the correct buffer and recoil spring?  There are too many variables to determine the problem without seeing it first hand.  Try Kurt at KKF.  

Yeah, first get it checked out and fixed on the jamming. As far as the ejection port door goes, that is not a necessary part. No need to replace the receiver on that account. You can smooth up the damaged area and just discard the cover if you want. I can't imagine a jam that would do structural damage to the upper.