[hef19898]

Short answer: obsolescence. The article hints at that, prices increased once the 707 was no longer considered a commercial product. I guess here, but the initial contract stipulated prize stability for a certain period after the last 707 delivery and them something about retirement of the 707 fleet.

Getting small quatities for obsolete aircraft parts, even in the civilian world, costs fortunes.

And yes, if it was (speculation) a new production run, all the manufacturing most likely needed re-certification: new production site, new production tech and so on. Maybe even certification to whatever standard was used for the original 707 / E-3, which might even be impossible (surface treatment that is now illegal due to EHS reasons, material norms being obsolete requiring new certification of the part using e.g. plastics with another norm...).

Plus the obligatory surcharge for the endless pockets of the litteral Pentagon.