The original module give some good points as to why Damocles was built in the upper peninsula of Michigan (page 11). These still hold true for the 3rd or 4th edition timelines. it will be interesting to read the re-write of this module updated for the 4th edition.
I like the idea of using the old missile complex as a DARPA black project site, but depending on the timeline used it is really close to active silos that would be targeted.
You also have to take into account that by START I/II agreements, all of these sites where to be decommissioned, so it would raise the interest of the Soviet Union (or Russia depending on the timeline) if one of these complex's showed signs of use afterwards. Erecting new above ground structures could be a problem.
An interesting place to look at is one of the AT&T L-5 Junction Centers an example here
http://www.missilebases.com/ballardmissouri. They are 4 story in most cases underground hardened bunkers. There where a lot of them around the country.