Welcome! Well, for not knowing anything about Commanders, you seem to have gotten one of the top of the line models. As for the engine, there's a shop in Elon, NC (IIRC) called hemiPros that will do a full swap with a remanufactured Hemi for around $3500. That comes with a 3yr/36K warranty. Whwn my Hemi goes, that's where I'm taking it. Best of luck!
06 Limited Hemi QDII
CBEngineering Coilover Lift Kit, tie rod ends, U+L rear control arms, RRO front UCAs, adjustable track bar, JKS QD sway bar links, Steel Armadillo diff cover and A/C armor, 4xGuard full Matrix, rock sliders, rear sliders, and belly guard, Wilco Offroad Hitchgate, all riding on ProComp Series 29 17x8.5 wheels with 265/70r17 Nitto Ridge Grapplers
.45ACP...because shooting twice is just, well, silly.