Nutloose, you're spot on.
According to Av Week (
Trump Vows To 'Negotiate' Price Of Boeing's New Air Force One | Ares)
The Air Force has estimated it will spend $2.87 billion in research and develop funds through fiscal 2021 on the project, and the Government Accountability Office projects the total cost will be $3.2 billion.
Think about that for a moment - ~$3 Billion in R&D - the actual aircraft are on top of that!
Boeing lost over $250 million building the current VC-25A aircraft - as noted earlier some of that was due to a poor program management, but much of it was underestimating the work required to meet the USAF requirements (adding things like dual APUs, aerial refueling, and EMP hardening to a passenger aircraft doesn't come cheap
)
As noted, I know more than I can say about the new aircraft requirements but if the USAF gets everything they are asking for, little more than the airframe structure will be common with a 747-8i. As I noted before, I was stunned at the level of system redesign that will be needed to meet the AF1 requirements - and that was just for the engines...