I know this has nothing to do with the actual setup and work that needs to be done, but I just wanted to point out that if after all that setup the intonation is still less than ideal, I have had good results by using the so-called "sweetened tuning" championed by James Taylor (and now incorporated into a setting in Peterson strobe tuners). You detune each string by a few cents (different amounts for each string). It does a good job of evening out the intonation problems across the whole fretboard so that it sounds passable everywhere. Many a problematic vintage guitar has been made playable again because of it. You'll find the specific cent amounts if you Google it.