Moon roof will not close via the motor.

Likely you have a blown "fusible link". These are located either near the battery + or the starter and can be difficult to locate.

Here's a description the sun roof
Power Sunroof System Components
The power sunroof system consists of the following components:
• Sunroof module
• Sunroof switch
• Sunroof motor, with 2 hall effect sensors and limit switch
• Sunroof window
• Sunroof sunshade panel
• Power supply for the sunroof module: RAP 25 A
• Ground G402

Override
The override function is used when needing to force a closing of the sunroof window. To override the system:
Turn ignition to ON.
Rotate the sunroof switch to the close position.
Press upward.
The sunroof switch data 6 circuit, or override circuit, will become grounded at the sunroof module. As long as the sunroof module sees this input, it will continue to slide the sunroof window to close, regardless of the other sunroof switch data circuits inputs.

This is normal. The reason it raises higher is due to the design of the sliding arms in the moon roof. without going into too much detail, the reason it raises before closing is to "unlock" itself from from the "Locked" open Position in order to get to the "Locked" closed position. Its a fancy way of making it seal well when closed and not rattle when open

There should be some way to manually close it. Look at the owners manual for help. All Power roofs that I have seen, has a small trim cover hiding a bolt or something like that. All it takes is an Allen wench or socket to crank on and close it. For more details
RV Roof Repair Leaks Repair

fist disconect all windows switchs install a new fuse and reconect the swichs one by one when the fuse bloout unplug that swich and check the others switch because maybe is one or more swichs bad.or you have a short most comun areas are on door hinges or one of the windows motor is burn out

Try disconnecting your battery. This will re-wire your computer and may clear the problem...

it has no emergency closing procedure. It could be the switch, the motor or the module. The latter 2 are on the moon roof and you have to lower the headliner for access.

Try to by pass the switch. Before you do anything, check the fuse.

check 30 amp green maxi fuse in fuse box under hood. just above 2 rows of 4 fuses in middle.

this should be #27 on interior fuse panel this also controls your power windows and interior lights

you have several options so do not feel screwed yet. first of all if you have the broken piece you can use clear epoxy and permanently glue it back together. Also, you can search on line or call a junk yard for the part you need.

will it work while in the ignition and running?