1. There is a max number, but I don't know what it is, sorry
2. As already said, you can send it by mail if it isn't bound
3. No, they all scale by level.
4. I don't think the hand phaser came from the C-Store, although I do remember a TOS bundle in the C-Store so maybe that's where it was from?? I can't remember exactly.
5. Yes in your settings. The setting is called Enable Gameplay Announcement Flybys.
6. The only thing I can suggest is checking out this trapped walkthrough. Maybe there is something you missed? If not then I recommend dropping the mission and starting over. If that still doesn't work then report it as a bug.