I just finished reading the module, it's pretty cool. Here's my thoughts on how I was eventually going to run it (SPOILER ALERT):
1. Use pregenerated characters for everyone. Change the names of the NPCs so that they aren't blatant ripoffs of almost every major Mythos writer in existence.
2. Summarize, either verbally or with a handout, the circumstances at the AFB, including the strange lights and cattle mutilations that have been going on for a while.
3. Do a brief narrative with the arrival of the van and agents, enough to get the PC's interest. Give the PCs brief opportunities to do small actions, both to get them involved and to give someone the chance to get guard duty later on (go lenient on SAN loss for PC guards)
4. Fast forward to the poker game, get people to actually play out a few hands IC and get chummy, good time to meet NPCs and get in the role
5. When the guards start to flip out, the adventure proceeds as written.
If the adventure seems weird coming from a D&D dungeon crawl type of perspective, just think of the base as an outdoor encounter area. The crashed ship, aliens etc are set encounters. The dimensional shambler and crazed guards are wandering encounters, and the arrival of the Ops team is the final event to end things.