You are normally better off panning the two mics away from each other. Then reperform the part and pan those mics opposite the first two. That way you have the close mic as the main sound and the far away mic as kind of the reverb on the other side (turn this mic down in the mix).
The phase switch can help, but since the two mics don't have the same frequency response, it is never a matter of everything being out of phase. Flipping the switch will just change the frequecies that are being cancelled. That might be good, or not.
As a general rule, the more guitar parts you have, the thinner they get. If you start adding more low end to the 8 tracks of rhythms, you are going to end up with a mess very quickly. I would try turning off the 3035 tracks, that is most likely where the phase is coming from (and the nasally honk) and pan the remaining four tracks left, 10 o'clock, 2 o'clock, right. That should thicken things up a bit. Always check things in mono, if something in the mix disappears, you want to know.