Love the idea of the question, although personally I find the scale quite large, but that's another post and no doubt a long one all together
Firstly I think the break down of teams needs to be looked at some, although I agree with 15% science and MARS I think that recon should be about 25% and 45% specialist and regional teams, remembering the project goal is reconstruction of the USA then we have to also assume that its more important to have a large amount of specialist teams like agriculture and engineering as well as strong and robust command and control. These more specialized teams would make sense to be frozen in larger bolt holes, maybe 12 man teams etc since their tasks require more bodies. This cuts down on a overall amount of bolt-holes.
Now hiding it..
Morrow Industries is vast and will be involved in building work all over the USA its subsidiaries will be decommissioning old mines, excavating water channels, installing seismic and weather monitoring stations, observatories, anything that involves lots of activity and digging in out of city areas. You could even include things like large retail parks on the edge of towns, specialty ones who are unlikely to be targeted.
In the MP game I am starting to run right now, the COT invests heavily in disaster relief both home and abroad and specializes in infrastructure rebuilding (best way to train someone to do something is to get them to do it firsthand). They have the Morrow Industries Disaster Relief Agency who throws huge amounts of people and supplies at these projects, they also slip in a few people to do security(MARS), evaluation(Recon) and development/prevention(Science) as well as aid with local agriculture and rebuilding of infrastructure(specialists) and all of them need to be co-ordinated and supplied.
This is a great source of ways to 'loose' people secretly, also a great need for admin, storage, warehousing, transport etc back home. No one is going to blink of they suddenly buy 20 heavy lift choppers etc.
The facilities themselves are great places for bolt holes as are the placing them outside of cities but close to transport hubs.
There is also the ease at hiding facilities along railway lines, there are large amounts of disused sidings and many area's that require industrial stripping to make them safe, chemical works, waste disposal area's, the list of places to put a bolt hole is endless, just limited by imagination. I mean in one module they put one in the leg of an oil rig!
I do think each regional area should have a larger store of personnel, regional command bases for example should have a couple of hundred, plus the same amount in frozen watch. That makes it easier since you need less sites, although you do need a few larger ones.
Hope this helps.
Earl