I guess its not really damaged, its just gouges from taking it in and out.

They should be faint scratches, not gouges. Mine is over a year old, and they are still just gentle little scratches. And my player gets inserted and removed from the sled about 4-6 times a day on average. Perhaps the sled is gripping it too tightly? Does it slide easily in and out? When you installed it, did the sled get bent oddly or did you have to cram or force it in there?

The "guide-bumps" on the sled that cause the scratches should be on bendable tabs that you can loosen. At least on the sides and top. On my old Mark1, I had to bang on the bumps with a hammer to loosen them (the Mark1 did actually get gouges and they did become a problem).

I also notice that the connector in the back of the docking bay kind of flops around a bit more then when it was new.

This is normal, this is covered in the FAQ.

I also noticed that the sticker that says warranty void if seal is broken is sliced because of the constant removal and insertion of my player. It would not be good if I ever had something happen to it and couldn't get it fixed because that sticker was broken.

This is also normal and is nothing to worry about.

Wow, I just noticed that the three FAQ entries I just linked are right in a row, one after the other, in the FAQ. What a coincidence.