*Update*
Almost everything is back in order - check engine light for EGR and QA upper limt and flashing GP light are gone! I ordered some tools and did the timing belt job, including the water pump, thermostat, fuel filter w/ tee, air filter, oil filter, new oil, and new coolant. I set timing between blue and green lines in VCDS. IQ was quite low - around "2" now. It would not let me adapt in VCDS. EGR excessive and QA limit codes still there at this point. Ordered seals for the pump. Man was this thing gunked up! The QA was completed coated in a layer of black "gunk" over 1/16" thick.. I will add pic below. I'm almost sure this is the result of running homemade biodiesel, or worse grease lol. The qa arm did not have fill range of motion, and the sliding control collar was also a bit sticky at the end of its travel. Cleaned it all up and installed the 3 main seals. I did not remove the QA from the housing to see the electromagnet etc, but there were no metal shavings at magent, and could see clean coils throught the little hole, so I left it alone. Primed pump, started, and adjusted IQ. Running good, so I cleared my codes and took it for a drive. The before instant check engine at startup is gone, and stayed off for the drive. Awesome! Let's hope it stays that way!
The only issue left is my air flow specified VS actual. They should be close, but specified (at idle) is 280 and actual is 480. Duty cyce is either around 5% or 85%. I have switched out all the vacuum control valves with spares and still the same. No codes for it. Even switched out the MAF for a spare and still the same values. Actual is always about 200 more than specified at higher rpms. I just cleaned the intake and EGR, and that EGR code is gone (only for one drive so far). I do have a vacuum leak I am working on fixing, can this cause it? Does the turbo affect these numbers? Or is it likely both the MAF sensors I have are bad?