OK, here goes. The speed density system, regardless of year is calibrated to a specific engine/trans combination, and when we do things like add cams that have a lot more overlap than stock (for that ballsy idle and mid and top end power), the vacuum signal drops which freaks the computer out. It's trying to compensate but doesn't know how because the timing and fuel table doesn't exist for the new combination. What to do, what to do. You scrap the speed density system and swap in the more flexible and accomodating mass air system with sequential firing just like the Mustang GT 5.0. They make a kit for the trucks that includes the harness, computer and mass air meter and it's available for 5.0s to 460s.
Now you can run the rumpy cam, big heads, supercharger, whatever without the EFI losing its mind. Better gas mileage too; stockers usually pick up 2-4 mpg over the speed density/batch fire system.
Another option is to put the latest MegaSquirt EFI on and have full adjustability with a laptop just like the more expensive aftermarket units. This way you can make the fuel and ignition curves exactly the way you want without compromise. Cheap but really good.