1. What is the OPERATIONS section of the game mat for? Rule book says nothing about it.
It's used for various episode cards. The cards themselves will tell you when to move something to operations.
2. Non-enemy verse cards. Do they jyst get revealed normally once they're pushed into the COMBAT ZONE?
If they are not scanned then all cards are revealed when they enter the combat zone. If scanned any events or other cards that have a reveal ability will trigger at that time.
3. Buying upgrades. The rules talk about choosing not to buy an upfrade, but say jothing about how they're drawn. Do I just draw the top 1, take it or leave it? Or if I choose not to take the top, can I keep drawing until I find one I want? (I'm guessing not this, as it's an overly cumbersome version of "choose 1".
Under the Inter-Mission section on page 16 there are the bullet points summarizing what you can do during this phase. It says to draw the top 3 cards of the upgrade deck.