I have Mockingbird ST, and I replaced the Ping Floyd Rose bridge and nut with a bridge and nut made by Schaller. When I setup the guitar, strings 6-3 are in good shape intonation wise, but the first two strings are off. I tune the open string to pitch with a tuner, and then when I hit the harmonic at the twelve fret, the harmonic is noticeably flat. When I intonate all of the strings, and then tune them with a tuner, the first two strings are always out of whack with the other strings, especially when I play chords. So, before I set the intonation on an individual string (fretting the 12 fret and matching it up with the harmonic), should I match the harmonic with the open string first? Or could it be that the nut height has to be adjusted?