First and foremost, well done and thank you for posting such a great write-up! Like Raybo, I am considering a 6.4 swap on a 2013 Ram 2500 with a non-MDS 5.7L but I have some concerns with going from a non-MDS to MDS system. I assume that my harness doesn't have connections for the MDS solenoids. In which case I believe that my options are to install an MDS delete kit (lifters, cam, plugs), or replace the harness and PCM. Since you've gone through the swap I thought that I'd ask what your thoughts are?Any tuner can disable the MDS. And the 5.7 already had the variable intake runners so the 6.4 servo plugged right in to the existing wire. The 6 speed is undoubtedly better than the 5 speed but that's a whole different project on it's own. In your situation since you have a 2006, none of the wires will match and you will run into a bunch of little problems. You're better off finding a 6.1 hemi that will pretty much bolt right in.
Thanks in advance!