OK first look at the front securing bar. There are 3 screws per side that adjust for height Use blue loctite on all 3 of them There are 2 screws in the bar and one big headed screw for height adjustment.
The trick is to get the height ajustment screw adjusted correctly and then snug the other 2 screws down without distorting the bar guides ( making the 2 screws too tight slows/binds the track guides on the sides of the front bar when the roof is in operation)this will happen if you over tighten the 2 securing screws. your really just trying to sandwich the big headed screw with the front bar, but only snug it. Use the loctite this will hold the screws in place.

For the rear use the locktite on the securing screws and try to get the blocks level with the track they might need to be pushed down a bit (NOT to MUCH as this will drive the sunroof into the car roof, when its opening) hence the plastic recommended in the other post ( you can find this hard clear plastic in most doctors offices reading magazines) The roof will usually scratch in the center so secure the plastic from the sides if your still having problems with the roof hitting try pulling the car portion of the roof up from the center gently this can sometimes make enough clearance

 

OK. I just wanted to update this thread for the sake of future generations and also for the people that offered help.

The contacts inside the switch were corroded slightly which allowed 12v to the motor but not enough current flow to turn the motor. I disassembled the switch and sanded the contacts. It is now working properly.

The reason I was having trouble with the sunroof after reinstallation is because I had installed the gates backwards. They will fit this way and the sunroof will work, just nor correctly. I had the left gate on the right and the right gate on the left. I have now fixed it and can actually see how everything inteacts with one another. It was a process but I now feel fully capable of fixing any sunroof issue in the future.

Thanks everyone for your help.

 

Yes this was it... if you had tested with the motor connected you would have seen no (or very small) voltage across the motor when active in the failing direction.

Without the motor load it may all appear to work correctly. This phenomenon is why its desirable to do initial voltage checks with equipment connected (possibly repeat with it disconnected and look for differences). However its often easiest to test things with the connectors removed... this is often far less accurate to the failing case - as here - and therefore misleading.

I have seen similar issues on cooling fan debug. A mechanic I know was testing the final stage driver voltages with the fans disconnected - everything worked fine - as soon as the fans were connected the voltage dropped to 0v (took him over an hour to figure out why it still didn't work). Of course the fan connections are hard to reach on the plug when connected...

Alan