Well just to thank everyone for the input and let everyone know I did get the problem fixed. Not the way I wanted to but it is fixed. After checking everything over several times along with a couple of friends it was decided we all had no idea as to why it was happening. So what I ended up doing is just getting out the die grinder and grinding a little off the inside of the covers at each spot where they were hitting. Hell of a way to treat brand new covers but it had to be done.
Anyway thanks to all for the input and info.