All Hemi engines will technically "Fit" in the JK. The issue is with how the front accessory system is set up. Check with the company whose kit you want to use to see if the kit works with that engine. The AEV for example recommends Hemis out of Cherokees and Commanders and JSS uses hemis from Rams.
I've been doing research on this topic and yes the 6.1 from the Charger will work but you'll have to change the oil pan and pick up. There are 2 variations of the accessory drives for the 5.7 (LX and DR) but one setup for the 6.1.
not knowing if your planning on keeping on the street or not, but doesn't the engine have to come out of the same year or newer for emission reasons?
That's a safe rule of thumb to meet 50 state engine swap requirements but rules actually vary state to state. For example, in Texas the only requirement is that the vehicle have all the emissions components that were present when the vehicle was manufactured.