John Y
I noticed the rear rail was certainly not lining up (from about the middle to the end of the LHS) to the contour of the toneau cover whilst trying to finish the soft top frame. Left unaligned the hood material would have have hidden things up but there would have been a very nice gap! The toneau cover I noticed does not have a flat profile.
Its been so long that I cant remember but it looks like the bottom rubber seals of the soft top frame rear rail must sit on the inner SS finisher/cap of the toneau cover. I cant remember where the hardtop bottom rubber seals sit on but by the looks of it they seal around the outer SS finisher/cap.
Despite this rail looking very 'bend proof' I managed to get it back into shape very easily with little pressure to match the toneau contour. The vehicle is on stands and I have just the right amount of room below the front tyre to wedge this rail under and bend my life away. Crude but effective but lots of care and a bit of skill required.
Moral of this story? Even though it is quite sturdy and well designed, if it does not want to move never ever force anything on the frame, it is amazing how easy everything can bend. Also I would avoid grabing the plastic caps when raising or lowering.
JY