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you dont have enough posts for pictures - hang out at the introduction forum and post up hellos till you can send a picture or 2 of what your looking at
No it does not go under, next to it. Depending on how many repop VS original parts you have on the bike, any one of them could be out a bit causing the interference. That said my chain cover has been "relieved" to allow it to be installed without rubbing on the battery box.