Brian Moore Low E Intonation Trouble

[Daniel Sorbera]

One of my buddies gave me his brian moore to fix (since I've been labeled the guitar repair guy ) and it's having some trouble with the low E playing intune.

I changed the strings, made sure it wasn't binding at the nut/saddle and setup the intonation so that on an electronic tuner it played perfectly in tune up and down the neck. But it still sounds "off". I'm thinking it's the guitar itself making some funky resonance/harmonics that are making the low E sound out of tune (because it's not out of tune when checked with a tuner.)

Any ideas?

[Mattia]

Tried moving the pickups a little lower? Is it worse in lower positions/open chords, or progressively worse up the neck (might be a nut intonation issue, check mimf.com/nutcomp for info).