I have been manually opening and closing my roof a lot in the last few weeks while I wait for a replacement roof module to arrive.

When closing the roof manually it always wanted to stop about 7" from the windshield. A quick search here provided the solution.
The pin and hook in the roof joint closest to the windshield were out of alignment, the solution is to adjust the rod connecting to the hook shorter.
Mine had virtually no adjustment left, it had obviously adjusted before and maxed out.

Opening the roof header up showed that the adjustment bar is a curved piece of mild steel.
It is the top metal bar in the pic below, (copied from another post). The length adjuster shown on the left.



I had to bend the rods on both sides to "recurve" the bar.
This shortened it enough to make adjustment possible, allowing the pin and hook to mate properly.


hook and pin

I believe the problem is caused by not manually opening the roof properly.
Rotating the manual latch release allen key counter clockwise until the roof latches release is not enough. After the latches release, the allen key also adjusts the angle on the hooks that latch onto the pins.
I was cranking it about 25 times, latches would release, and I would open the roof.
With the cover off I could see that actuator hadn't moved half of it's travel.

It took 66 complete rotations!
Its a soft stop don't keep forcing it to see if you can turn it more.

After a full 66 rotations the hooks will now clear the pins when the roof is opened manually.
It appears that the mild steel bars were being slowly bent a little more each time I opened and closed the roof, without fully releasing the latches.

Lesson learned, keep cranking to the end!