We typically leave the DC of the injectors out of the calculation unless some odd application is apparent as since we are pulsing at an IDC it's a relative item.

For example, if you have 650cc injectors(4 cyl) at 90% and want to spray 25%, you would use 650 of Aquamist injector. If your car is at 90%IDC, then the Aquamist, barring any gain/trim adjustment will be at 90%IDC as well.

So your two engines with 440 and 550 injectors, would use different size jetting to deliver the same amount based on IDC readings.

Other than that, once you get you jet amount, I would add 10-20% for pumping losses. The jetting chart is ideal conditions, depending on how you set your system up(tubing lengths tee's, etc.) each applications losses are a bit different.

Here is a page laying out a few samples:

http://www.howertonengineering.com/Jet_Calc.html