Regarding the idea of trains switching out in some sort of tunnel or underground rail yard, modern diesel locomotives put out an astounding amount of exhaust (and older units from the 70s and 80s, which would be when the most work was going on, would produce even more exhaust) so what would be needed is an infrastructure of ventilation ducts and gigantic fans to keep the air fresh for the workers as well as to allow the engines not to choke on their own exhaust. Such ventilation equipment installed on an out-of-the-way mountain would arouse suspicion. The very first item to be installed in such a facility should be an massive air purification system, unless the ventilation is camoflagued so as to appear a natural part of the mountain, or emplaced under overhangs.
Another idea would be purchasing a seldom-used rail line (which would then be a private and wholly-owned subsidiary of Morrow Industries, Ltd, naturally) in the mountains where plenty of tunnels abound and assembling a tunnel-boring machine in a large tunnel, unseen from the air, then creating a side-tunnel and excavating an increasingly larger subterranean space for storage and operations; the occasional train run on this line would have empty coal cars either topped with black tarps to suggest to satellite imagery that they are loaded coal cars, or be painted black. A trainload of empties would enter the tunnel on one train; simultaneously, a loaded train with the cars filled with excavated debris would prepare to leave the opposite end of the main tunnel. Any satellite or aircraft watching this progression would see a "loaded" coal train entering the tunnel and then see that same train leaving the other end of the tunnel after a suitable interval. Locomotives involved in this transaction would be painted with identical markings so as not to raise suspicion when Locomotive 1234 enters the tunnel but Locomotive 5678 leaves...
The train could continue on the Morrow main line to a point where it intersected with another railroad, then taken to a Morrow-related destination where the excavated materials could be used or dumped (i.e. landfill, or another Morrow excavation which needed tons of rock to cover it up). And over time, suitable strengthening could be made of the rail line so as to allow Class A railroads some trackage rights and then get their hands on really good stuff via intermodal traffic and manifest trains. As well as the occasional trainload of military equipment and vehicles being transported from a military installation to a firing range (I am thinking, for example, of a mountain redoubt between Fort Riley, KS and the NTC at Fort Irwin, CA).
Might even give Morrow Industries a tidy little profit...thus paying for the excavation out of other operating funds to help hide from government oversight until such time as the revamped line can, via trackage rights, pay for itself.
Additionally, rail fabrication equipment, concrete tie stacks, vast stocks of rail equipment can be stored in the mountain and then rolled out after the nuclear strikes to help fill in gaps in the U.S. rail network, or at least the portions that the Project requires initially.
Finally, to take a page from United States railroad history, a few thousand Chinese laborers can be frozen in the mountain and then thawed out to gandy-dance their way to prosperity in the post-apocalyptic frontier.
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