So why did it take so long to cough this guy up?

Served in the Navy and law enforcement in Sacramento area isn't that large a set. Something isn't being reported correctly.

This seems more like they got his DNA, and then backfilled the correlations.

While it may have worked in this case, it's more than a little worrying because it changes the police from "finding the correct suspect" to "justifying the DNA identified suspect".

And we already have a case in California where the police let the DNA guide them to the wrong person.