changing the pilot jet will effect which main jet you need. if 110 is good right now and you decrease the pilot jet, its possible you will need to put in a larger main jet.
i personally think the ideal tuning route is get your pilot setup correctly then setup the main jet then tune the needle. though, i know some people (including 'professional' tuners) disagree on that though. though i have never heard a real reason on why you would tune main jet first then pilot jet. just the reason of "thats how you do it". i guess blind trust is good enough for most people.
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