Rain stopped and I finally got it figured out. Turns out the side marker lights have two female connections on them. One is ground the other hot. There is only one wire that runs to them and it is a hot wire. If you connect the hot wire to the wrong connection on the light, Poof, goes the fuse. Man do I feel stupid right now.
Anyway, got it figured out and atleast I have all new lights on the trailer now. I went with the Digital LED water proof lights all around along with all new wire from truck to trailer. I even changed out the truck plug with a LED plug.
An expierence I will never forget, so I guess I learned something from it after all. Thanks all for you input, it helped alot even if Im not the smartest fish in the pond.