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What is the combination to get my windows to go all the way up? After raising the top the windows only go 2/3 up. Is it raise and lower the brake lever twice while turning the rear view mirror 90 degrees and sit cross legged in the seat or what?

Perform the "battery disconnected" reset procedure in owners manual.

If this doesn't fix it, something's broken--go to mechanic.

The top latch is not properly locked.(microswitch)

That, or the microswitch in the latch is fubar. I have one on order because my windows drop to that position if I hit a hard bump. I un-latch and then re-latch the top and I can put the windows back up.