Just a slight thought on exhaust blockage (which I really doubt it an issue, but possible!).
The engine was out right? the exhaust was open right? Was it anywhere other than your shop during this time? Could be something accidentally got dropped in there. (or even accidentally on purpose once it was discovered that they were not going to be able to ho$e you on replacing the engine, but again very doubtful, but still possible!)
OK now back to the leaks ANY leak in the air charge/cooler system is a problem! Get that air charge cooler fixed! I'll suspect that once that is done and you verify the rest of the exhaust / turbo system is in good none leaking condition it will perform like a new engine! (oh yeah it is a new engine!