Repairing roof question..

The caps don't fit nice and tight like I believe you are thinking. They fit kind of loose and sloppy, allowing the caulk tape to fill in the gaps of random size. You are using caulk tape right? I would not try to reshape them unless you think they got warped in transit. I don't have a picture of my caps handy but they are "OEM" originals and they matched the ones I took off other than the hole locations seem to be a little random (not drilled while in a jig). The overall shape is the same. Are yours the same as what you took off? Their fit isn't perfect but when you add the caulk tape that is about 1/8" thick, it basically fills the gaps to make them water tight. After you set them, then you can run an additional bead of DICOR around them (not the bottom edge). The top of these are radiused and the roof is more square, this is where you will need to double up the caulk tape as you see fit and squeegee out the excess by pressing down (bedding them in). The screws along the side will finish the rest. You don't need to "crank" them down to get all the caulk out. Use a blade to remove the excess before caulking.

I'm assuming you are doing this with the roof closed normally. Only work on one corner at a time to let the others support the roof construction. The sides should be perpendicular to the roof. The front and rear roof edge are angled outward slightly. The roof sides should be resting on the box sides. This should make it all sit correctly. Unless your box is twisted, then you have trouble - this may be where the mishaped is.

I'm hoping this helps you.