According to my testing, you can't move the Flight Controller around too much. Seems the right side of the FC must point Fore or forward. You should probably also keep it parallel to the front edge. Shifted FC to the port/left a bit. Installed RX radio next to it and GPS module in front. You can get parts ( FC, RX, GPS, and taller Power-Board components) close but they should not actually be touching. Just securing with foam tape for now. Test fit cover.
If using your own micro-usb cable during testing (directly into FC), be sure metal connector is long enough to fit all the way past white FC case (plug mates completely).