If I'm reading this right, you're recommending an 06-08 motor. Do people swap the heads from the 09 and up motors to the pre 09 motors since the heads flow better? Is that even possible?
'06-08 car motor is probably the most cosmetically pleasing to most people (myself included). Simpler coil pack setup, and better looking car intake. Also does not require messing with anything VVT related. You will more than likely have to delete the MDS, which I believe is a lifter swap, not sure if you can use the factory MDS lifters. Others can chime in on that. If you have no interest in A/C, I would recommend the car motor.
I've heard you can swap the Eagle (09+) 5.7 heads on the earlier 5.7s with the right head gasket, but I have no experience. You can't just swap them on or apparently your compression goes through the roof. Like I said, I have 0 experience with this. Keep in mind, you would also need the 09+ intake and exhaust manifolds (different shaped ports).