Ah yes, the joys of fixing the busted plastic guide rails and sliders on the sun roof!
Most likely the plastic alignment sliders have broken and thus misaligning the entire track when it needs to slide backwards. Often more than not the pop up rods got bent also and popped out of the busted cracked pivots where it holds it into the sliders.
Might need to do one of the following.
1) purchase a Lincoln LS sunroof repair kit and attempt to disassemble and replace.
~ Would involve drilling out some small rivets and redoing them.
2) go to a scrap yard and cut out the headliner at the out edges and undo the entire rack.
~ also not fun and don't damage the end drain tubes on all four corners because if they do get broken, you'd need to drill out rivets as well.
Possibly could be that you have a motor issue but if it makes a clicking sound when it reaches the end and does not pop up or when all the way forward closed, it fails to pop upwards for the vent position, it then points back to the plastic guide cracked and broken which in turn hold the push up metal rods, which tend to get bent when was forced into the pop-up position while is was jammed off the tracks while sliding.
I ended up picking up the repair kit for mine but since then got a steal of a deal on an entire sun roof rack with motor and glass from a scrap yard. One of the end tubes for the drainage got damaged in my forceful removal of the rack out of the donor LS so I'm now forced to undo a rivet anyhow to swap over one corner end drain tube. (was trying to avoid this but failed)
In order to fix this jammed cracked sunroof, the only choice is to drop the headliner and remove the glass then proceed to get the entire rack out on bench and start working on replacing the busted plastic rail guides. No way around it, can not be fixed while in car.
It's rather intense ... sorry to say.
Sun roof repair kit from the Sun Roof Doctor =
http://www.sunroofdoctor.com/0002lincolnls.htm
~ lots of fun! GLWR
