I wouldn't be concerned about the reprogramming as there were some TSBs for reprogramming to correct or improve performance.
2006 Steel Blue 5.7L HEMI Limited 4x4 Build Date: June 9, 2006 Hour 14
Interior: Dark Slate/Light Graystone with Saddle Brown Leather Seats
Quadra-Drive II, NAV, DVD, Trailer Tow Group IV, Off-Road Group II, Remote Start, UConnect, Rear Backup Camera, Chrome Wheels,
Magnaflow cat-back exhaust, Daytime Running Lights enabled, 2" Rough Country Lift with 265/70R17 Goodyear Wrangler AT/S