Ok, so far, I have tried blowing canned air into the cd changer, and using a "store bought" cd instead of a burned one, and it definately works better.
One thing I noticed is that the passenger side front speaker sounds weak and crackly. It does not do this when I use the radio, only the cd player. At first I thought it was the amp causing it, but now I am not sure.
Tomorrow I am going to buy a cd lens cleaner and see if I have any luck with that.