OK.
1. Speck of dust can be fixed for 5 bucks at any watch stall.
2. Scratches on clasp can be fixed with a scotch brite pad and some Cape Cod cloth.
3. Link pin can be pushed in by finger nail most likely. If not, dry a small screw driver, apply pressure with flat side.
4. Crooked marker is barely visible. If it bothers you, send the watch to a modder, it's fixable.
5. The pearl would bother me as well. Get in contact with Mary, maybe she'll offer to send you another insert? Or buy one for a few $ on the bay.
On another note let me add:
You have a keen eye for detail. Congratulations. Try a gen. They're perfect!
Val.