On my guitars, I find with distortion - as you probably have in drop tunings, fourths and fifths need to be very close to the overtone series or the overblown harmonics will object adamantly. Thirds need to be on the dark side as well and probably be way out to your ears. If you use your standard guitar tuner, the thirds and even octaves will be brightened up. Needless to say, powerchords will beat mechanically. You may have to go with a custom just intonation. IOW for the key you're in and avoid clashy voicings.