Installed Berk HFC's, car is going crazy... help!

[Red370]

well, today I installed my Berk HFC's, now im having all sorts of problems, I hope one of you can shed some light. Before install, I unplugged the negative battery terminal to reset the ECU, it was unplugged for approximately 4 hours. Well I reconnected the battery and the car cranked up like a champ, sounds great btw. But I went to get out of the car and I noticed my window when I got out wouldnt seal. I also now cannot roll the window down when the door is open. Also, while the car is off, when I tap the push ignition, when all the lights go out, the SES flashes, then stays on. I hope I didnt just open a can of worms, has anyone else experienced this? Also, my windows wont roll down with the key fob anymore...