Yeah you should have your chip reburned. The current program might be fine for Naturally Aspirated trucks, but your supercharged truck needs more fuel and less timing, and a N/A truck needs more timing and alittle more fuel. Also with your shift kit AND the chip it might shift too harsh, as usually you need to let the burner know that you already have a shift kit..
So yes, I believe you do need to have your chip reburned, but I suggest NOT going with Superchips, and trying JDM,Chris Johnson, or PSP, as these guys either deal with Lightnings(JDM,PSP) and I've heard nothing but good things about Chris Johnson's chips.
Thanks Lightning Struck. It feels good to have someone actually answer this question. Its seems that there isnt' too much knowledge on the subject, or maybe nobody cares. I will see if I can get of hold of Jim or Sal.