Just want to update this thread. After I rehooked everything up it I got it working. I didn't have to do anything different but I noticed the indicator that comes up on the dash that shows how much brake it's applying, doesn't come up when the truck brake is depressed even though it activates the trailer brakes. However if you use the squeeze bar just enough to get the indicator on the dash to pop up, you can then see the trailer brakes working while depressing the pedal.
All in all, I believe this was user error and nothing was wrong.