I'm familiar with a supercharger kit for my other car, so I'll share this-
You'll want to drop one or possibly two heat ranges on the plugs, and gap them down as well. I would go as low as .040-.045. With too big of a gap, the supercharger will 'blow' out the spark. A lower temp thermostat is not a bad idea either, but the ECM would need re-programmed.
As far as the fuel system, most blowers will either re-program the ECM or add a FMU(Fuel Management Unit). What the FMU does, is add more fuel when there is more boost. Otherwise, the engine will run lean and BOOM! About the injectors- I'm not sure what the Jeeps come with, but I would try them out first before upgrading. Not sure about the fuel pump either. It might need upgrading instead of the injectors, 'cause if the fuel pressure can't stay up... Boom!(again).
Just keep a real close eye on the A/F. If it drops, back off. Engine rebuilds although entertaing for everyone else, are not fun for you.
Peter M