Intonation Problems
Instruments- discuss specific features, luthiers, instrument problems & questions
Three dimes seems like a TON of extra height by the nut. I hope that isn't due to warping or bowing.
If you have a nice straight edge on a metal yardstick or something like that, you could set it along the fretboard and observe if the straight edge touches all the frets, or if some of them are lower/higher. It is possible that some frets have risen slightly out of their slots and need to be 'tapped' back into place.
It can be helpful to check each fret with a tuner and note how out of tune each fret is. If the first couple of frets are the most out of tune, the issue is most likely your nut being too high. If the frets get more out of tune as you get closer to the octave, you most likely need to move or reduce the height of your bridge.
Once the frets are all level and the action is correct, you will most likely have to readjust your bridge placement anyway.
Tune the string up to tension and get it exactly to the desired note. Use a tuner to compare the open string to the note at the 7th fret (octave) If the octave is flat, the bridge needs to be moved *closer to the nut* If the octave is sharp, the bridge needs to be moved *away from the nut*