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I'm not familiar with this particular model but it sounds like you ran the motor past the track limits. You will have to take it apart again and reset the motor onto the track, as well as reestablish the track limits for raising and lowering the sunroof. I'm not sure how familiar you are with doing this kind of work, but you would do well to get a factory shop manual in order to do it correctly.
It's not a particularly brilliant system. When you hit the switch, the motor will keep running until it hits the contact on the track that cuts the power. If it doesn't, or the contact is in the wrong place, it will run off the track and then just spin. This true for both directions. Did you notice either of these when you replaced the motor? The shop manual should be able to tell you how to set them correctly.
Is there any debris in the track of the window especially towards the front. Thew clicking sound you are hearing may be worn gears in the drivve assembly of the window/power roof mechanism. Is there a limit switch for the sunroof? This may be bad also. Check the easy stuff first and get back with me.
It can be faulty motor or loose wiring issue or faulty /weak sunroof controlling switch or there is some blockage for sunroof to come down to close or sunroof out of its track the headliner is out of its way.There re many possibilities.All this basics needs to be checked.For further troubleshooting,go through this help link:---- Click the link mentioned below:------ How to Manually Close the
Sunroof ?http://howtobyme.blogspot.in/2012/05/how-to-manually-close-sunroof-on-2001.html
Could have possibly came off track, you may try having someone from outside the vehicle try gently pushing the sunroof toward the close position as someone in the vehicle presses the close button. Hopefully with some luck you should be able to get the roof back on track to close.
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