Sooooo....this is almost certainly not all Boeing's fault, and they may be less at fault than the government in this particular case. Presidential aircraft are very unique and come with a multitude of unique and complex requirements from self-protection to C4 to self-sustainment, and all of it has to meet standards that far exceed commercial ones and likely some 'regular' mil ones.
Throw in the fact that several different agencies/entities each have their own requirements outside the DoD, like the Secret Service, it makes things that much more complex. The fact they weren't built from the frame out as VC-25's likely complicates things. And having seen it myself, those requirements have likely evolved/changed and been added on to over the years. "
Wait, we need this capability now...."
One only needs to look at the VH-92 procurement as an excellent example of how the new VC-25 procurement unfortunately isn't unique.
According to recent reports even though all VH-92's have been delivered it maybe until the end of the decade that they will fully take over the mission.