Awesome! I appreciate the input. There were definitely some things odd about the controller that I noticed when opening it up. First off, one of the screw covers looked like a replacement and it appeared to have been re-glued on there. Also, the screw posts were glued together as well which meant I had to pry open the controller after removing the screws. When I was trying to remove the screws, they were in there really tight and I ended up stripping one of the screws and breaking part of the post while trying to get it out. Since the post was already partially broken at that point, I went ahead and broke it all the way around. I had to do that since the screw was stripped and it seemed to be glued in there. After finally taking apart the shell, the top board was also glued to it's post! Whoever took it apart before thought it was good idea to glue everything pack together for some reason.
Anyways, I emailed Bradley and Bruce asking if they had replacement pads and Bradley responded saying he couldn't find any for the Pro Controller but they will try to look for them. He also mentioned that I was the first to ever ask about replacement pads for the Pro Controller.
Edit: Also, I 'll open one of my SNES controllers and see if the shoulder button pads will work.