I'm thinking it's a MBC problem. They aren't really that great of a control solution, and aren't the most consistent devices either. A boost leak on the main piping or wastegate should be easy to spot and usually easy to hear, and you're having a problem building boost so it may be a problem with the wastegate control. That's why I would take a long look at the boost controller.

I guess my biggest question is have you actually looked at the boost response with a boost gauge, and is it having problems building boost or is it just low on power with a normal boost response?