The wires in the jamb are not running through the OEM boot??? Your description reads like either you poke a hole in the boot on each side (door and car) :face-icon , or you got the wire inbetween the grommet and the metal of the car!
As in most cases, (but definitely in this one) you want to follow the OEM wires and go through the boot. It is definitely not a particularly easy or fun part of any install, but that is the "right" way to get wire into doors.
glennQ