unfortunately i dont think there is a way to accurately get the guitar to work. This is due to how the emu "talks" in ps2 language. the section responsible for pads always says "yes there are 2 pads plugged in" not "there is 1 pad and a guitar" or anything. part of the recognition is that constant axis which you are experiencing, which also makes mapping very difficult.
i have yet to find away around this, wouldnt mind either cos i love GH :/
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