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i get that it's monophonic. no chords. i'm playing very slow, simple lines. when i hit a single note that i simply want to sustain, it will glitch into an entirely different note within 3 seconds half the time. the other half of the time i get lucky and it doesn't glitch. i need predictability though.
It sounds like your level just gets too low to track. Try increasing the input level to your H9, you can do this in H9 Control or by pressing and holding the left footswtich while moving from Active to Bypass. Alternatively, you can try boosting your signal before the H9, or using some compression before the H9.
Also, imerkat had some good suggestions, neck pickup and tone roll off. The neck pickup will give you a more sinusoidal like note, and the tone roll off will help with low-level interfering noise.