Your pilot jet is too lean. What size are you running. I live at 7,600ft. so I can't really recommend a size. The quiet popping is normal. Full on back fires are not. My bike is set up almost exactly the same ('93 XR6, supertrap, uni-air, and overbore). It does the same thing when you let out of the throttle. Also make sure the engine isn't running to hot, which causes pinging. Read the many articles on the internet about reading spark plugs. I think there is a tread on that right now in this forum. Good luck.
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