Okay, so I've managed to sort of splice the chords and the harmony into the same channel, and I think it doesn't sound half bad to my surprise. On the other hand, I can't seem to get it to work at all for the second half of the song. On square 1, it kind of takes the backbone out of the song which leads into my problem with square 2, and that's that they both have the same rhythm, so it sounds way too choppy.
In general, the timbre of the arpeggios still sounds bad. (<octave 4 50% square arpeggios at full speed usually sound bad, btw. You can try other timbres, you can try a changing duty cycle over time, it could be to do with the volume, etc. This is of course my opinion, but maybe you'll find something you think is more interesting too by experimenting )
pattern 03 row 24, I think that you should either forego the second note of the diad to play the backing chord, or somehow intermix the two.
pattern 06: I believe the backing high track is still diads or chords, could mess around with evoking that idea.
pattern 08, row 24 on: Is the original track really doing something as simple as playing the same note twice on two channels, and nothing else is available to imply? In general the end of this pattern feels weak.
Nice. Keep growing better and this and all your stuff will be great. Now your arps don't bug me at all. Good work on that.
In notes clash, try making a chord out of it(I don't know, if there are two A-3s, make one of them a E-3 and you'll get a chord, which will sound better that a clash).
If chords don't work, change the Pxx in one of the channels and perhaps the duty cycle.