Well I think I kind of did it, for the problem is largely contained. I'm rubbish with the relief so I just skipped that part and worked directly on the truss rod, empirically. The notes became flatter when tightening. Now even the worst notes are not sharper that 1/8 and many are fine. I'm not sure how close to the ideal pitch they should really be, but for now I'm happy. Probably it's worthwhile investing in a set of those nut files.