It will ride one day and you will be happy, don't worry.
1. what you call the “compression plug” goes on the bottom of the fork cone. It is the centering ring for the lower bearing. Once you have fitted it, the head tube will no longer rub on the fork

. (look attached picture)
2. the marked part is the centering ring for the upper bearing. The recess must be at the front for the cable routing.
3. can you explain again about the seat stays or take a photo? I don't quite understand it (may be due to the language, sorry).
4. write to Velobuild Support, they will send you a replacement part very quickly.