"modify the intake threads to seal properly. " Boy that is worrying..... ooops, I guess you knew that already! Sounds like he filed the holes in the intake? Perhaps he found that the end cork gaskets tend to make the intake set up too high and he filed the intake holes so that he could start the threads in, and then pull down the intake with the bolts.
Which makes me wonder if he pulled the roll pins inserted into the end sealing surfaces of the block (the tops of the end walls of the valley), if they are still installed. If they are there, and he did not pull them, the intake may be damaged/warped at the ends now. The roll pins stick up vertically out of those end sealing surfaces about 3/16" or 1/4", and are used for alignment of the stock intakes on many (all?) of these blocks; but the aftermarket intakes don't have the matching holes. And that would cause sealing problems too.
