Just for the other readers out there, I found a replacement Pump and controller on ebay for 220 shipped. Threw in my car, hooked up my vag-com reprogrammed the controller for the settings i like (roll windows down with my key....etc) and it works fine. The only problem was, is that i was so excited that i finally figured out the problem, (water on the controller) that i cleaned up the water and dryed it and didn't look any further for other problems.... mistake #1. Well about 4-5 months later during the rain season, my key stopped working remotely again
SO, i immediately go into the trunk and check out the pump/controller unit, and what the F*#! do you know!, theres water down there again!, ya i was pretty pissed, so i bit the bullet and bought a third (yes third) pump controller off of ebay for 200. Comes to find out that the drain from my gas tank cap (that little hole below your gas cap) was clogged up down by the pump/controller and when it rained, it would back up and drip slowly into my trunk..... So i took out the hosing, blew it out with compressed air, cleaned out everything i could see, sealed the rubber gromet that held the hose against the side wall, and NO problems anymore! Lesson learned for me, but cost a little money. Oh well, hope it helps someone else for troubleshooting in the future.