Yeah, it was all the way out of its casing and coiled up in the left rear quarter panel (it came out from the previous owner holding down the switch until it eventually just pulled the cable out, not from being damaged). I took a closer look at the motor and managed to feed it in a little more so that both gears are turning, but the roof only goes up half way. If I operate it manually it goes all the way up just fine. I set the slip clutch to let go at a very low amount of torque (I loosened it to the point the arms couldn't lift the roof, then tightened it a little bit at a time until they could lift the roof without the clutch slipping), so hopefully I wont be stripping anymore gears. I'm glad I bought 2 sets of gears. I stripped 2 trying to get this stupid thing to work right
It also seems that the passenger side arm is always off by a tooth. If I take apart the gear box, correct it, then put it all back together and try again, it's still off by one tooth