Dayne - I listened to about half of this tune this morning. Are both the rhythm and lead guitar parts done with the same guitar? The reason I ask is that the lead guitar is either not in tune with the rhythm, or its intonation is seriously f*cked. I could hear where you were trying to use dissonant notes, its not that. If you used different guitars, or if the parts were recorded at different times, then that might explain it. I can only seriously suggest (again) that you get an electronic tuner - this will let you tune to the same frequency every time. You mentioned before that you knew you were tuned to A-440, but why?
I've got a number of different clip-on tuners, and they generally work ok - event the one from Reverb.com that cost $3. My favorite, and the one that works the best is the Korg Pitchclip:
http://www.sweetwater.com/store/detail/PC1 I like it because when I fold it down, it practically disappears when I leave it on the headstock of my Taylor. I've also got a Korg Pitchblack pedal for stage use
http://www.sweetwater.com/store/detail/Pitchblack .