O-P
I was right in the middle of the VC-25 program (the current Air Force Ones). They were so heavily modified from the run of the mill 747-200 that it was estimated they cost ~$500 million. Each!
Heck, when I was troubleshooting engine issues on the first VC-25 we were informed that dropped tools, etc. had
already done over $500,000 damage to the executive interior
.
Since it was a fixed price contract for a small fraction of that, Boeing took a financial bath on the program.