Well thanks for the help but I am still having problems. I took me a while to find the alignment hole (until I removed the screw that was in it). I did align the inner gear while the rear part of the roof was up and the switch control did change but the forward switch movement still makes the roof open, all other switch directions seem to work except that the roof still pops up if i use the up direction from an open position. Don't know if that's right or not. Should the motor cut out when the limits are reached ? I still hear the motor trying to move the panel when its all the way up or back. I wonder if there is a possibility if the wiring at the switch is massed up, since they had to remove the headliner.
Ian