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If you're doing the Megasquirt tuning yourself, just keep an eye on your duty cycles, and you'll be fine. As a stop-gap measure, you can adjust the fuel pressure regulator (for ITBs, you are changing the regulator, no?) and bump the pressure up a bit. 60psi or so should see you a reasonable increase in injector flow, but settle on a flow rate before you start tuning.
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