Justin,
I guess there's probably several dozen ways you could integrate NDT into the mix. As stated before, it sounds like you have done your homework on a lot of this, so hats off to you for that! My personal suggestion is to try to find the way to make your program effective, BUT keep it simple at the same time. I'd personally keep the CT3M about the same, and start NDT treatment at 2x per day; breaking up 1 grain, 1-1/2 grains, or whatever dosage you establish with your physician ...
If you feel you need a little more cytomel T3 during the first week, then that option can always be there. If you did 1-1/2 grains you would be getting approx. 14mg of T3 (If my thinking is correct), and it won' take too long before additional T3 is converted from T4. I don't think you will need any extra T3 beyond what you are taking with the AM CT3M, and of course what will be administered from NDT, but like I said before, we're all different, so you will just need to pay close attention to how you feel, body temperature, and of course labs.
On Isocort, as far as I know they just stopped producing the stuff. I heard something in the rumor mill about a new formulation like you had mentioned, but nothing in concrete. I requested some input from Bezwecken in OR, but they won't respond on the matter.