My last car had most of the things youve listed there, and it would run a whopping 4psi on "stock" boost. I needed a boost tee to actually get it up to the standard 7psi. Funny thing is, they had a boost cut at 12psi with a buzzer that went off in the cabin when it hit... I could get my guage to read around 11-11.5psi when it hit. It wasnt leaking boost, it simply just didnt run would it should have without help.
I dont know if wastegate actuators get dodgey over time or not, but this car was in the same age bracket.
I just had a thought, if the BPV(s) was leaking and recirculating back into the intake, could that cause it?