I think you're going to get mixed answers on this.
2009+ started the VVT and requires a cam phase lockout of some sort in order to do a cam swap, unless you want to keep the VVT and know someone that can tune it. Pretty sure there are some engine management setups that can tune it (maybe Holley? Not sure). 2009+ heads definitely outflow earlier heads and will respond better to a cam swap.
2003-2008 has the earlier heads, non-VVT, however some do have MDS. MDS can be easily deleted, and cam swaps are cheaper. All 2003-2005 Hemis use the coil packs that fire opposing cylinders at the same time while 2006+ coil packs fire the same cylinder and get rid of the rats nest of plug wires. No performance difference between the two from what I've seen, but just cosmetics.
As far as car or truck, yes the truck accessories are higher and tighter to the block so there are typically no clearance issues with the frame or anything and you can run A/C. I believe with the car engines you have to notch the frame rail to clear the alternator (or run a Jeep alternator or something), and I don't think you can run the A/C compressor in the factory location. Truck motors already have the main cap stud to support a mid-sump pickup, and some people are using the factory pan with aftermarket k-frames. A lot of people like the car intakes better for cosmetics.
