The cartridge bearings should both be the same. If a 45 degree bearing is installed upside down, it would ruin the seat in the head tube quickly and probably create a huge gap.

Most headsets come with a few .25mm shims that are used to increase the space between the headset top cover section and the head tube, to prevent interference. Be sure that there are not any of those being used. If not, there'e little that can be done, other that recutting the top seat (assuming it's part of the head tube and not removable - some brands do have removable seats in the head tube).