KenV,
Eisenhower was quite clear what his concern was: "the economic, political, even spiritual" well being of the nation and the "very structure of our society" and "our liberties or democratic processes." He did not address those interests converging "to protect and sustain capabilities that the nation did not need."
I think you glossed over Eisenhower's overarching concern:
In the councils of government, we must guard against the acquisition of unwarranted influence, whether sought or unsought, by the militaryindustrial complex. The potential for the disastrous rise of misplaced power exists and will persist.
This is the concern the F-35 program evokes in its current structure that's being ignored by the councils of government.