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the sunroof motor is simple to replace, but may be time consuming. you first have to remove the headliner. take all the trim holding the headliner off to bring the liner down. once you are inside the headliner, remove the two screws holding the sunroof control assembly. Disconnect the wireing harness from the motor. 3 screws hold the motor in place. Before removing the motor, make sure the sunroof is closed and sealed shut. the motor is timed to the position of the sunroof. Do not turn the motor gear under any circumstance. once the motor is out, inspect the drive cables for any visible wear. Installation of a new motor is just the opposite of removal. the new motor should come pre-timed to the "Closed" position.

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Q: How do you fix the sunroof motor of a 98 Saturn SC2?
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I'm not an expert but I can tell you what I did. The sunroof on my wife's 95 Saturn sc2 would not close all the way, had to reverse it and try again several times to get it to close. This was in 1997 and it was still under warranty. The dealer replaced the track and it fixed the problem. Have to keep the track lubed, they have a certain grease at the dealer they recommend for this. Then in 2007 it started the same thing again. After finally getting it closed it would not work period anymore. The motor didn't even make a sound. I took it to the dealer for a transmission problem and asked them to look at the sunroof too. They said it would cost upwards of $800.00 to $1000.00 to fix and to tell my wife just to leave it closed. They said the whole thing needed replaced. I worked on it myself, have to take the headliner frame part of the way down to access the motor and wiring and the black box which I think is the relay module. I started testing for power at the switch and moved on. I had power to the motor but it didn't make a sound so I thought the motor was bad. Got a new one at the dealer for about $190.00. Went home to install it. When I took the old one loose the gear on the motor was kind of binded with the spiral rod that it drives to open and close the sunroof. I got it loose and plugged the motor back in for the heck of it and it came on. So I reinstalled it and the sunroof now works. Took the new motor back to the dealer since I didn't need it and talked to them about my experience. They thought it was odd too. We figured what may have happened is since the motor gear and the spiral gear jammed on the last use the motor heated up getting the sunroof closed and tripped the relay but it didn't reset for some reason. If you operate the motor back and forth continuous for a little while the motor heats up and trips the relay but it resets itself after the motor cools down. It is supposed to anyway. It still works, every once in a while I have the not closing all the way issue. I reverse it and try again. A few tries and it closes. I just make sure not to overheat the motor now. And make sure I lubricate it regularly. Not sure if this will help you out or not, just thought I would share my experience with the sunroof problem.