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Anyone have any good methods of practicing the piece? I think I have issues putting both parts together; I can do the multiphonics, but I guess I don't get how to check both pitches

Try learning the intervals note by note. Assuming you've already practiced both parts separately, the difficulty comes in, as you said, checking both pitches. This is primarily a listening issue. the majority of the intervals in Fnugg are perfect 5ths and unisons. Obviously, it's quite easy to tell if you're playing in unison, but a 5th is a bit trickier. If you have a piano or keyboard nearby, I would recommend playing the intervals broken apart note by note, and then together. Once you get the sound of a perfect 5th in your head, the rest should come relatively easily, as the melody and harmony move together by steps. Regardless of what interval you're playing, it all comes down to being able to hear the notes both separately and together as one unified sound. Hope this helps!

it does.