Well, I think my underboosting problem was two-fold:
(1) When I had my protune, Jorge noticed that I had a temperature issue where my car wasn't cooling down fast enough - it would linger above 200 much longer than it should before finally dropping. I also noticed that occasionally the car's dash temp gauge would read toward or at the higher middle tick mark and stay there before dropping (usually immediately after driving the car hard for a short period of time), so I think I had some air trapped in the system or I had a tiny leak or crack which was allowing air to get in OR I had a faulty part somewhere. I can't really pinpoint the exact issue, but I think I solved it now because the temp stays near the lower middle tick mark all the time. I had the coolant professionally flushed for the first time around 90k (up until then I was just emptying it, rinsing it with only distilled water, and refilling it every 30k), replaced both radiator caps, got a new all aluminum radiator w/ silicone hoses, water pump, stock thermostat, and replaced almost all of the small coolant hoses that I could see.
(2) My stock TD04 had almost 94k on it and the fins were beginning to contact the inner housing.
I think the occasional complete lack of boost problem was my car's ecu attempting to limit power due to high coolant temperatures. I think the slight underboosting problem was the worn out TD04 losing its efficiency.