Yep.
Whodunnit?:
Col. Mustard in the Kitchen with
The chain. There were 3 links that were problematic (subtle bend or tight), as in they had been smashed by the derailleur at some point. They looked fairly straight along the chainline but made noise when they were going through the rear derailleur and guided onto the rear cogs.
The slightly misaligned front derailleur did not help nor did the
worn (but not too worn) middle chainring.