Guess what? I wasn't crazy. Turns out the engine was experiencing a loss of power/torque, despite everything appearing completely normal. It was build up behind the exhaust valves and in the exhaust manifold that reduced exhaust flow and thereby effectively reduced the displacement of the engine. And it became a self-reinforcing cycle: The ECU still “thought” it was moving the expected volume of air, so fuel delivery stayed the same = effectively richer mixture, lower power, more deposit formation. So the engine was running rich ever since the problem started and the richness only continued to add more deposits. This rich condition was undetectable because this engine consumes such little fuel to begin with that we're only talking about a difference from maybe 4.2 GPH to 4.5 GPH, which could have been easily justified by temp/air/seasonal differences.
We did an exhaust leak-down test early on, but that only told us it was sealed properly, not that there was a partial blockage.
This was discovered after I finally decided to have a top overhaul done and the cylinder heads and valves were pulled apart. The cylinder heads and valves themselves appeared fine (which is why it always passed borescope examinations), but once the exhaust valves were removed from the cylinder heads, a significant amount of stuck sediment fell out. Now that a top overhaul was done and the cylinder heads and valves reconditioned, the engine can breath properly again.
To ensure this condition isn't repeated, we have added an Annual checklist item to remove one of the exhaust headers and borescope inside the exhaust manifold to check for and track build up.
It only took two years (and about $10,000 of troubleshooting), but mystery solved.
Posting this in hopes that this may help someone in the future.