you can unbolt the glass section of the sunroof. There are 2 trim pieces on the right and left from memory, remove them (think they just have a clip holding them in, pull that out and with a bit of force they should pull down)
2 or 3 bolts behind that on either side, glass section will pop up (The sunroof is fully closed for this to work)
once you pull it out you should be able to see if you can run it back and forward then see if you can spot the issue with the extra space you have
Otherwise take a look at this thread:
http://www.skylinesaustralia.com/forums/topic/206252-sunroof-issues-fixed/
Hope that helps