Crazy my just did the same thing, auto up to the top and then drop to within an inch of being fully down. I did the reset twice but only rolled the window up to an inch or two before it was closed. Seemed to work. I might have done the rest in reverse. Can't remember for sure other than I was...
I know it's not the same but here is what I am running. KCs with the RTR endings on a stock modular bumper, height of the openings is the biggest problem. Modified the heck out of the brackets and made some spacers.