How to deal with high frequency distorted guitar?

I need to check with tuner when I press the string on higher frets... maybe that's the reason indeed...
 
Hmmm, I tuned my guitar while holding the chord, and still sounds like in this clip... maybe it's because of the played intervals...
 
Hmm, there's no way of post-processing it somehow? Now it's like this dissonance is louder than everything else. Thanks for feedback.
 
Temperance tunning is a bitch like that. Even if the each note in a chord is perfectly in tune, the chord will sound out of tune, major chords are the worst at this as the major 3rd sounds sharp to the chord when it is in tune.

Nothing you can do but deal with it, unless you want to get a guitar with a tempered neck.
 
OK, so I guess I need to record these parts playing more separately and try to mute when going to the next note... Anyway, thanks for feedback.