[bobcowan]

The first thing to do is set your balance with a synchrometer. If it's even a little bit off, it won't run well.

With a carb, you have pump squirter's. When you step on the gas pedal, they give an extra squirt of fuel for the added load. EFI needs something similar. I have a separate map based on vacuum load and rpm. When the vacuum goes down, the computer adds extra fuel. Seems to work pretty well.

You'll need to look and see how the ECU manages air pressure changes. I'm not really familiar with that system, but it must be able so sense and adjust for ambient air pressure. If your AFR is correct during steady driving, it's probably fine, and probably not your problem.