I would say you're getting way ahead of yourself. Don't even try to do final adjustments (or even just trying to get things close) while still running open headers.
The dynamics do not compute... And they certainly do not play well together.
So get your FULL final exhaust setup, set up, then play with carb adjustments.
Granted, you might still find you need to do the same things that you're contemplating already, but you wouldn't know until you spend the time and energy to do it. Then find out you have to do it all over again, if anything changes due to the additional exhaust restriction.
That's my take anyway, on doing anything without the full exhaust on it. Not just for EFI, but applies to carburetors as well.
Paul