I was always told that to straighten out a hole you had to bore it, or so that is what we do at work.
Your problems raises a perplexing question... now, obviously the hole, the threads and the countersink all have to be about the same axis. Given that, on a swamped barrel... as long as those three conditions are met... should it matter if the axis of the hole is normal to the bore, the bottom surface of the barrel or the top surface... other than aesthetics... I don't see any reason... am I wrong?
I think Captchee hit the point well, unless the countersink is about the axis of the hole and normal to the hole... ain't gonna fix it.