Having "mostly read" this, I honestly can't believe you had so many problems and are digging into some of these tables so much. I've had MS3 Pro on my 340 for 10 years a month from now. With multi-port, coil near plug, cam and crank with sequential injection and spark. It was very very easy to get it "good enough" and not have many quirks straight from the beginning.
Almost all tuning I did was in the VE table, Spark Table, IAC table (IAC target with temperature) and the PID. My car basically just works and other than occasionally surging when you tip in an extremely small amount at a low speed with the clutch out, I can't complain. Even got 21 mpg doing 75 on the way to power tour and 19 average on the trip.
My car has all GM sensors other than the crank sensor (Ford Ranger) and the Cam sensor (5.2 magnum distributor base). I understand some of the things about the Dodge specific sensors and all that but for example you can send injectors out to be flow tested if you don't know.
For the A/C I just use the A/C idle up to add 150 rpm. The PID is able to deal with any deviations and gets to the target fairly quickly with "Engine States" known. Heat soak doesn't seem to bother mine whatsoever anymore. I had too much prime at high temperature, which is how I dealt with it, it acted like it was flooding.
I am even using overrun fuel cut, controlling the fans, controlling the reverse lockout for the T56...I have ground speed control included as well.