First, they checked the dynamic advance and it was spot-on, so it's not a tuning issue.
The wastegate and actuator were both checked and they're working properly, despite the damage from where the actuator arm was scraping against my Cobb turbo heatshield.
A compression check was done - passed - my engine still has a clean bill of health.
Next, they thought maybe the catalytic converter in my Cobb downpipe was blocked, so they swapped my dp for a catless one they had laying around (it's a bit dented, but it still works). After that, I picked up several more psi of boost (probably because it's less restrictive without the cat and the 3" to 2.5" taper), but the car still underboosts noticeably.
Finally, they used a boroscope to look at my stock turbo internals and they found out that the fins are actually scraping against the inner walls of the turbo due to some play in the shaft. Apparently, this is a fairly common thing in higher mileage turbos, but that's what they ended up saying was the cause of my slight underboosting, so it looks like I'll be getting a new turbo (and some other goodies) in the very near future.
I have a tentative appointment set up in early May for a turbo install and a tune the following weekend. I've narrowed down my choices to:
1. TD05H-16G-XT Blouch turbo w/ gaskets, Cobb SF intake, and tune
2. TD06H-20G-XT Blouch turbo w/ gaskets, Injector Dynamics 1000 cc top feed injectors, IAG BigMAF intake, and tune
Right now I'm very seriously leaning toward #2 because that was my goal from the very beginning and now I finally have a chance to do it. If that doesn't fix my underboosting problem, I don't know what will