you say it has the air intake through the OHG?
there a flexible rubber hose running from the airhorn to the base of the OHG. We had a brand new truck come in the shop back when i worked for yale that did this very same thing, it wound up being that hose. For some strange reason it was collapsing just enough to change the airflow into the engine and causing it to run very badly. We removed the hose and truck ran great, put it back on and engine would run badly.
Might want to give this a thought and see...
since you say removing the air filter made a drastic change in performance. Also check the airway in the OHG and make sure nothing is stuck in it restricting the airflow.
It sounds like an air flow restriction problem.