I don't know anything about B-52s, but I work on a project where we are essentially replacing a 40 year old weapon system with a new one. The new one should of course do the same things, preferably better, and do additional new things. The old system started out simple, but has since had most of its internals swapped both hardware and software wise a number of times. We have full access to all the documentation of the old system, but let's say there has been periods throughout these 40 years where this aspect hasn't exactly been top priority.
It doesn't come as a surprise to me that projects like JSF end up a complete clusterfuck. Everyone tends to underestimate the complexity of the system they operate/produce after a while because most of it is always there and just works.