Okay so preliminary results are in. Switched the wire over to 2BE and as expected i no longer get the window problem and no check engine light! However the original problem remains
Going from p2 to p1 the pump goes off for a split second. Now I dont think this matters but it might. The red wire from the pump goes directly to the battery. Then i taped that wire for the red input wire on the controller and put a 10A fuse in there. Would that cause my problem?