1) view boilers racks down in the vendors section, excellent rack, and if you need custom options he'll work with you, also blackwidow and several other rack manu's still have racks for KJ's
2) flowmaster or magnaflow or any other top line 'free flow' work great as a clamp in or weld in
i run a super44 and love it, i don't notice the drone at highway speeds, you don't really hear it if you ride with the windows down or stereo on at a normal level but the drone is there, so take your pick with the Tommudd option

3) X2 on what tom said, keep the stock box and work up a cold air intake with dryer hose / LTT intake mod and a quality (non-oil) filter
4) if you're talking about stock mopar rock rails, you're pretty much right, added that they have a plastic cover that will get torn all to pieces over time on rock, the mopar steps, mount surprisingly strong, but unfortunately hang down about 6-7" or so, but made out of steel so you can always put plenty of rash on them in the process of getting "real rock rails"

Rusty's and boulder are still making rails, boulder attaches to the pinch (makes them much stronger) rusty's attach like stock mopar STEPS, which is strong, but nowhere near as strong as one using pinch attachments, however, the rusty's bars should be easily modifiable to attach to the pinch should you go that route
No idea if RL still has rails in stock, i was told several times that he was done with rails but it would be worth a double check
5) check the tire/wheel and fab section, there's a ton of stuff dealing with crag/blackrock as well as other rims that people have used / discussed as well as stripped down and repainted to their liking - fitment and rub issues will greatly depend on your lift and tire combo, but go ahead and pound the pinch and get that over with

Looks like you got a good list and game plan going!