1) Gotcha. As you mentioned on Twitter, I think making Objectives their own kind of card – one that is always placed last in the corridor – would make that rule clearer. And would also allow you to introduce new Objectives for variant games or "expansion packs", as you said.
2) I think a rule like "+5 points for each non-Essential, non-Backpack Gear equipped" sounds good.
3) I'll play again at lunch today using the new rules (+5 points for gear, and only subtracting number of remaining Threat cards).