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Have you asked JKM their thoughts, Steve?
Hopefully it's an easy fix like plugs rather than fuel pump but that's why JKM turned down my Revo settings after fitting the much more demanding Twintake, so I wouldn't have the expense of a HPFP. A more efficient aftermarket air intake is going to change your air to fuel mix. But I don't know how the startup issue would be caused. Surely the map plays a part?