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There is always some back pressure. When running a supercharger if you make intake or exhaust changes i.e. ported throttle body, adding headers or in your case changing axel back muffler sections. Unless its an identical component it will affect airflow and thus affect your fuel/air ratio. I would put it on a wideband A/F guage and log it to be sure but if the boost guage changed. There's a reason it changed. Remember more restriction will show more boost, to a point .
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