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1) Technological advancement. BEM brings back prototypes of advanced technologies, but that is really little more than a sales gimmick. Someone still needs to invent them and develop them, because time travel doesn't allow for knowledge to come from nowhere. And then you have to invent all the supporting technologies (and there are a LOT) that support all those inventions.
Take the portable laser weapon described in 3ed. Right now, state of the art laser technology would cost me a cool million for a laser that is the right size, but is nowhere near powerful enough to serve as a weapon. Then I would need to add the environmental controls (so that it doesn't melt itself) and a battery pack that would make state of the art modern batteries and capacitors look like something that came out of a pyramid. Heck, we had to tear a small satellite apart because the launch got delayed by a year and we knew that our batteries would have degraded too much in that short amount of time to be viable for the mission duration. And those were expensive, expensive batteries.
Or fusion power. We have already spent many, many billions on fusion power and are not within a century of what TMP needs. Forget about the fusion packs for a moment and consider just the one type of fusion reactor the Project most needs - a unit sized for vehicles with enough power to operate the vehicle and its subsystems, with enough fuel for at least a couple of years. That requires incredible work to first develop the impossible and then develop the advanced materials and techniques required to miniaturize them all.
Add to that the cost of developing all of the tools needed to make all this stuff, because that often gets disregarded. I could make a truly amazing laser right now... if someone would only invent a way to manufacture optical antenna arrays at lambda/2 spacing, and ways to efficiently produce the kind of precision optics. Tooling get surprisingly expensive.
And while people often think that they can use civilian costs for comparison, you really can't. You're buying for an effort that cannot afford for equipment to fail, because it might not be replaceable and someone might die when it breaks. It needs to last a looooooong time on the shelf and work perfectly when you need it. It needs to operate with minimal maintenance and parts, in conditions where you can expect ash, and radioactivity, and combat conditions. This stuff is
expensive.
2) The size of the Project. 50,000 people in the Project? If we go with the assumption that 40,000 of those are in field teams, and that there are an average of 8 people per team, that is 5,000 field teams. Each one needs their own bolthole, 6 unique caches, and at least 1 vehicle (preferably two, given the dispersion of the Project). Each bolthole has a fusion reactor, as does each vehicle, so that is 10,000+ compact fusion reactors, 35,000 excavations, and 5,000+ large, militarized vehicles that need to be acquired and modified.
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You make a lot of assumptions that I don't see as being the only path forward. If Bruce is smart he will bring back tech items that can be made with the manufacturing technology of the 1960s-1970s. For a person with the genius of Bruce it would be obvious that bringing back anything that requires a huge investment in new technology or exotic tooling is going to increase costs and reduce security.
I look at it this way. A 16 year old kid can turn smoke detectors into a functioning neutron gun in a shed in his mom's back yard using nothing but simple tools. It cost Billions of dollars to run the Manhattan Project, but once the basic principals and materials were discovered the investment has been made and the science and technology may possibly be produced more easily, more cheaply and on a different scale.
If I was Bruce I'd either have items specifically designed in the future for construction in a series of war surplus factories in 1965 or at least ensure that all the really hard R&D had been done. For all we know a fusion reactor could cost no more than a jet engine, or even no more than a high end Color TV set.
As for land purchases. If this was my project I'd buy up land right off the go. Land won't get any cheaper. Any surplus can probably be sold at a profit. A bolt hole will be expensive to build and fairly large but a cache is about the size of a basement for a standard house, or even smaller. Until they get loaded up they are just concrete boxes in the ground. There are huge numbers of such things serving dozens of purposes all across the civilized world. No one really notices them.
If the project bought up a lot of form military land no one is even going to wonder about concrete boxes in the ground, unless they find a bolt hole. In fact buying up former military property during this period makes a huge amount of sense. Here is a site that has a list of abandoned airfields, many of which are ex military from WW2.
http://www.airfields-freeman.com/
I'd have to ask folks from CAMP (Council on America's Military Past
http://campjamp.org/ -which used to stand for Council of Abandoned Military Posts) for a good list.
Advantages
Many in the middle of no place
Often are already fenced and secure locations
May have bunkers that can be converted into caches or bolt holes
Digging can be explained as removing UXO, waste, or demolishing bunkers and other structures
Cheap
If areas can be marked as impact areas they can be easily restricted
located all over the place, in every state
If digging takes place before the EPA is created in 1970 there will be no restrictions. A lot of these bases don't even get looked at, if they have been yet, until the last 25 years, so well after the war in classic.
This won't solve all the land issues and the issues around building infrastructure but it can help out a lot.