Strange one, since the bolt does not look to be glock cut, and really would double check the feed ramp insert in the lower receiver to make sure it was set all the way down to start with. If the ramp is part of the 223 mag well conversion device, then would double check to make sure that the conversion block was not set too high in the lower receiver.
Hence the part missing from the math, is that lower receiver to begin with, and if not a dedicated 9mm lower receiver, then what mag well conversion block in place next.
As for if the feed block is correctly milled and set in the dedicated 9mm lower receiver (again, not part of a mag conversion block), then would use a mill to make the needed cut to the feed ramps to get it to clear the bolt. You can use the file game for final clean up with a few strokes, but removing a great deal of material with a fill temps to look like ass in the end isntead.