Since it is a chassis dyno, this is a possibility. What does the rpm graph look like? Does it blow right through what should be peak hp? How does it drive? What is noteworthy?Converter or clutch needs upgraded.
I’m to lazy to read all the stuff about valve springs or turbos being the object of confession.
The OP is dead set it seems that he has checked all engine possibilities and all of it checks out. If that is the case, it has to be turbo's or drivetrain I'm guessing.
Were there any significant changes to the IAT's between the old and new turbos? Confident that the boost readings are accurate and consistent between the two engines? If the air quality and pressure are similar, there should be no HP difference from the turbo's.
Possible that the dyno is at fault? Again, you ought to be able to feel the difference on a drive.