I always recommend anyone check cranking compression of a motor, even if you didn't build it. Pull plugs, kill fuel/spark, it gets you a check to ensure that cam timing is ok, etc... for the sake of just getting the car to run at idle, I doubt something is wrong since it runs in open loop. I run 180 psi cranking on my 307, but with EGR enabled, and the computer does okay. I won't say great, but okay. I get around 15 inches of vacuum at idle in gear if I remember correctly.
As you're experiencing, CCC issues can be a nightmare, especially coupled with vacuum leaks. My system has an occasional stumble the first time it goes into closed loop from a cold start, 1 out of 5 times it will die if I'm not in there to blip the throttle and raise the idle level for a second (choke is already off). Within 2-3 seconds it is back to normal. I've never been able to diagnose it on a scanner, swapped ECM's, changed parts, rebuilt carb to CSM specs, etc... so it is what it is.
Enough about me, on to your issue... I don't think the cam is too big. The advertised numbers @0.006 are fairly small (256/268) and it's on a 112* LSA, so this thing isn't huge by any means (as evidenced by high vacuum while idling in open loop). Vacuum is vacuum to the computer. If it sees what it needs to (16-18 inches at idle) and the TPS is in range, it's going to try to operate out of the correct lookup table in the PROM. I'm really surprised that you only see 12 inches of vacuum, unless it's running so poorly that it is misfiring and causing the car to run like crap. The 15 inches shouldn't cause a big enough issue initially that would cause the system to freak out and run horribly. I would be slightly concerned if your cranking compression is higher than 185, as you'll potentially see pinging under high load/low rpm conditions, but that shouldn't be affecting your startup idle immediately at closed loop.
I also don't think a custom PROM chip will solve your issue, and that's a really expensive guess. I'd be willing to bet most people here saying it's a custom PROM issue wouldn't want to place the money on the bet for it unless they had a free one to test. That's also not to say a bad PROM won't cause the issue. A member on realoldspower (username Prop Joe) had a 226/230 Engle in his 403 that he could get through Illinois smog with the original CCC system, and it has around 9.5:1 compression. That site has crashed several times, so the thread is long gone, though he is still around. I remember him mentioning that the car wasn't much fun to drive in this configuration, but you had to do it every 2 years to keep plates active. He ran it normally with the CCC system disabled and replaced with conventional parts.
Since you didn't build the carb, it's hard to know where the MCS rich/lean stops are set, what passages have been drilled, etc... I'm suspicious of issues there since you already had one dead MCS after the rebuild, and a passageway could be clogged (with a shaving aka barry grant style) or a parameter way off. You can check all those settings with the thexton tools that are now obsolete and hard to find. A low float level may be masked by the open loop startup parameters. If you were local I'd be happy to help.
I would also recommended testing all the vacuum systems with a handheld pump/gauges. Things like stuck EGR, bad carb pulloffs, leaking valves to the canister purge system, etc... can all add up. A lot of those systems are on thermal vacuum switches so they don't activate until the car warms up, suddenly you have a big issue that you think is CCC related and really has nothing to do with it, because it activates around the same time as closed loop. Also, are you sure the secondary butterflies are seating and not causing a vacuum leak there?
As much as I hate to say it, everyone here, including myself, is guessing. The drop to 6* dwell is trying to compensate for a lean signal from the O2 sensor or an input from one of the other sensors that is freaking it out. A scanner may be helpful here so you can watch a real time data stream so you can see the inputs the ECM is receiving.
It's your car and your call. I'm not a lover of the CCC system, and would probably remove it if it were me for a conventional Q-jet and HEI. However, you have a lot wrapped up in building a mild engine to work with the system, and I'm guessing 1 or 2 minor things somewhere in there is ruining the whole experience.
Hope you work it out, and hope we are able to help somehow... I've been in your shoes chasing issues hopelessly and eventually got lucky (or found someone who knew more than me). Good luck!