CC Roof operating windows on offside after roof malfunction problem

[Peter King]

We had a problem with our 2007 roof not completing it's fold down (opening) cycle last Friday. Roof went down but had 2 bars on the dashboard display still to go. That's when I noticed that there was something wrong with the boot final locating position. Off side was slightly up compared to near side. After doing the youtube search, I was able to do the emergency roof lifting procedure. First step, after lifting the boot lid, is to insert the allen key into the front middle of the main roof section. This is virtually impossible unless you've got very thin arms but that's another story. From there you pull back the boot trim, find the two wire loops that attach to the release lever. Done that okay. This allows the boot lid to be tilted backwards as per when the roof is being operated. You do need two people for that procedure. Had I been able to reach in far enough to release with the allen key, ordinarily I should have be able to lift the roof up and secure in the closed position. Fortunately for me, I was able to see and resolve the problem of why my roof wasn't able to complete it's fold down cycle without having to lift the roof. On the offside hinged mechanism, there is a locating pin that should come to final rest in the forward most part of the mechanism. What had happened was that the plastic circular guide had come out of its locating position, consequently blocking the recess hole for the pin to go into. From there, I was able to put the boot lid back to its folded down position in the correct position. This in turn, allowed the roof folding down cycle to complete. With the dashboard now showing complete, I was able to raise the roof back to it's correct closed position.
Happy days but I didn't want to attempt fait so left the roof up in its closed position. Tried up my local Ford dealership to see if I could buy a replacement plastic guide. No such luck, no longer serviced part come up on the system. Decided to glue the old one back on until I can get a 3D plastic part made.
At this point I thought I would give the roof another try. Now I've discovered that the offside drivers window will only fold down the minimum distance as per when opening the door. The offside rear passenger window doesn't move. This is turn, doesn't allow the roof to fold down. If I manually fold the two offside windows down via the main window switches in the door rest, the roof will operate okay. I guess there's an electrical component somewhere that instructs the windows to fold down when the roof is required to be folded down.
I don't know any thing differently, but initial thoughts are maybe the roof operating system needs resetting or perhaps there's sensor or switch giving problems since the original malfunctioning roof fold down problem. For the record, the nearside windows operate correctly when the roof is being operated. Have thought about having a look to see if there's a switch or sensor in the roof mechanism that can be swapped over from the nearside to the offside to potentially find a faulty component.
Anybody else had similar problems that could potentially give me some pointers as to what is wrong please?