[bouncytruck]

Do you have a single or double wall top? When installing my top, the holes in the aluminum bed rails lined up with the holes for the single wall top. Is it possible that you have the brackets reversed?

The rear aluminum strip sits right at the corner of the body on mine. If it weren't raining like crazy to day, I'd snap some pictures.

The windshield track was lame. I mounted it with the far ends down as low as possible into the rain gutter. This left the center about 3/4" or more above the rain gutter. In the end, it works without any issues, but it didn't seem right when I was installing it.

Sounds like you need to spend some time on the phone with STC. My kit came complete and install was fairly painless. It did take a long time to install, but I double checked everything before drilling.