I haven't even been to Novac, yet, but out of curiousity, I went to the Strip and had a talk with Mr. House. The very nature of his secret, the person he mentioned (Who is Benny?), and a quest update telling me to find and kill the guy who tried to kill me in the Strip don't make much sense to me. Did I accidentally fast-forward the main quest by daring to see the Strip? What's going on? In which order should I be doing the main questline?
Also, where can I buy a passport for the Strip? Is the 2000 cap payment at the gate a one-time payment or do I need to pay it each time I enter the Strip?
It isn't a 2000 cap payment its just a "credit check" meaning you need 2000 caps to be let in. You can buy a passport for 500 caps from the shop in Freeside after passing a speech check.
It sounds like you missed the Khans in Boulder City, but they don't say much. Benny is the guy in the intro that shot you, which should have been explained earlier on, though you could have missed it. You're still pretty much on track for the MQ, so I wouldn't worry about it.