There is always more than one way to do things. It sounds like you have changed quite a few things, and to at least some extent they are cancelling each other out.
IMO, to reduce a touchy pedal with large injectors, start with what HP tuners call the part throttle governor tables. This limits the initial amount of fuel that is delivered when the throttle is pressed. Next work with Boost Limit A table to keep the smoke down.
Be careful when modifying the duration (Main Injection Pulse width) table. If you notice on the stock duration table, that the minimum duration is 160us (other than 0). This is because the default value in the ecm for a minimum injection event is 160us. If you command less then that, the ecm will skip that event. This is probably the largest cause of rough idles with large injectors. It's also one of the reasons that some tuners go to single event tunes. With large injectors you will probably at the very least need to reduce pilot injection, so that the ecm can deliver at least 160us during the main event.
As far as a course of action... Go back to the stock pedal maps, and stock duration table. Adjust the two tables I mentioned, until you get the off idle, and acceleration the way you want.
Adjusting the duration table down to match the larger injectors, just means you end up with stock power with the larger injectors. If you wanted 10-20% less fuel, then you should put 10-20% smaller injectors in it.
Again... More than one way to skin a
cat...
Paul