The reason the cruise control surges is, in control system terminology, it has too much gain. It is calibrated for stock injectors and the stock ECM, so when it senses that speed has dropped, it sends a command to the VP44 to increase fueling by "X"%. With the bigger injectors and box, that signal is intercepted by the box and changed to, maybe, "X+20%" (just to pick a number out of the air). Now, the larger injectors may actually deliver "X+40%" in response to that signal, so speed increases much more than it would with a stock truck. When the cruise control senses this speed overrun, it chops fuel and the cycle repeats itself.
I've seen some posts about a way to recalibrate the cruise control by turning it on and off or resetting speed a number of times, but I can't recall the specifics right now. Maybe someone with the shop manuals handy can dig it out.
Rusty