The rhotic harmony seems like it could work. How would they interact (if at all) with rhotic consonants (i.e.'r's)? Perhaps a reset?
I still think it'd be interesting to have an alternative distinction between consonants besides voicing, for example aspiration or palatalisation (I also just remembered prenasalisation, which could be interesting...); these could perhaps interact with vowel harmony in their own ways.
In the presence of two independent vowel harmonies, I won't bother suggesting throwing consonant harmony into the mix...

N.b. the tilde is in the 'combining diacritical marks' section of unicode; Times New Roman/Arial/Courier New should have it and some other fonts may as well. They can be accessed through Character map if need be. The tilde beside the letter is still comprehensible though.