Special K - thanks for giving us updates. I happened to take a look at the service manuals for the GT yesterday and looked up some diagnostic information on the problem you described.
In the engine diagnostics there is some guidance on troubleshooting problems like no start, long cranking, rough idle, etc. But there is also a section on reduced power and some reference to diagnosis through specific sounds. A discernable "chirp" sound points to the blow-off valves. As ItalianJoe accurately pointed out, there are two of them on the GT. That's kinda interesting (the fact that there are 2) but perhaps even more interesting is the fact that they are electronically controlled. Hence, I suppose the reason that ItalianJoe was referencing the importance of engine management software. (In a lot of different applications, blow-off valves are completely mechanical.) Anyway, based on a very, very, long arm's length diagnosis, my gut still says issue is in the "charge-side" turbos. Despite that the blow-off valves are electronically controlled, they are still physically opening a valve (when commanded) and my bet is on the mechanical side of one of those valves not fully closing. It may get pushed closed and sealed under higher, but not so good under partial boost.
In terms of the findings of the broken/melted/cut vacuum line(s) to the wastegate, that is a good find. Vacuum leaks are never good and really need to be dealt with before continuing further diagnosis. I'm skeptical that this is the root problem because an errant wastegate control will compromise the creation of boost... but typically doesn't having anything to do with releasing charge-side pressure (save for the fact that a vacuum leak could obviously be problematic.) Typically a vacuum line to the wastegate is originating from an ECU-controlled boost solenoid as opposed to true manifold vacuum. I'll explain. For example, let's say that the target maximum boost for a Ford GT is 20psi. The wastegates would have a physical spring of about 1/2 of the target maximum boost pressure - so say, 10psi in our example. It means that under hard acceleration, the turbos would generate 10psi of charge pressure and then the wastegates would start opening to vent the exhaust gasses and boost pressure would level off at 10psi. (This is what is meant when engine builders say the car was running on wastegate springs.) But, in our example, we may want 20psi of boost. What happens is that there is an ECO-controlled boost solenoid. The ECU will control this solenoid to add pressure the wastegate diaphragm. This pressure becomes additive to the resistance of the wastegate spring. So, at full song, the turbos will ramp up to 10psi.... but then the ECU can add 0 to all of this 10psi back to the wastegate resistance and now the boost pressure between 10psi and 20 psi is being completely commanded by the ECU via the boost control solenoid.
So, coming back to your car/problem. If the vacuum line(s) that they found are true manifold vacuum, they need to be corrected and there is the possibility of this being the entire problem.. Fingers crossed! But two things that can throw a curve at this.... if the vacuum line that is cut/broken/melted is coming from the boost control solenoid, then it is not true vacuum and would more likely compromise maximum boost attainment as opposed to an un-warranted release. Th other nagging issue is that the sound sure sounds more like the bypass valve "chirp".
Anyway - I wrote way more than I was planning but maybe it provides a little more insight into the foundational elements of turbocharged engines.
I don't actually own a NGT, but I've been thinking about getting one.
