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This may be an issue in the transition blocks or with the cable itself. I need to know if this is a regular cab, supercab or supercrew
They hold the cable in place and align it, if they have slipped from the blocks, this will cause it to not shut or open all the way. And it is a pain to get to. You have to lower the headliner and removed all the trim. And you have to be very, very careful that the cable doesnt unspool or you have to replace the regulator and motor. See attached diagrams and directions
It truly is a pain. The headliner is that piece on the inside on the roof(see attached)
Yep, that it is. Lovely Ford engineers at work... No problem and will be here whenever you can get to it.