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Re: Power sunroof
Pry open your wallet 
The motor is behind the sunroof between the headliner and the roof. It is driven by two cables that are (for lack of a better way of putting it) ribbed. The motor drives the ribs and the cable is attached to the track.
Usually the issue is the guide at the end of the track breaks free (is soldered) from the track and allows the roof to skew out of square. Once this happens, the class binds in the track and the cables "skip" in the drive assembly...this is the clicking you hear.
Your best bet is a complete assembly (minus the glass) which wholesale is about $1500.00. If I remember, the retail if you don't have a wholesale account is close to $3k.
You can get some replacement parts, but it’s a pain in the neck to get everything working again.
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Steve
'98 JGC (ZJ) 5.2L, Aluminum Radiator w/Electric Fans, 4" Cowl Induction Hood Scoop, Custom High Flow Air Filter, Magnaflow Cat / Flowmaster Super 40 Exhaust, Engine Oil cooler w/ remote filter, In-roof 8" DVD, Profile 600 Watt Amp, Kenwood 6.75" 3-ways, NV242, 3.5" Lift, RS9000s, 31x10.50x15 ATs, Proline roof rack w/ spare tire mount and 4 Hella 550s.
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