I've read through this several times and what I surmise you're saying is the the BOTTOM edge of the header port actually blocks some of the exhaust port on the head. Is that right?
That is correct. It fits the rest of the port fine but the lowest portion of the port on the head is hitting that short wall from the header port being to small. Im curious on if this is hurting performance/high rpm hp at all. I would say its a good 1/4" wall...going by memory