THREAD CONCLUSION
Per my last I want to conclude this thread for now. I had hoped to implement the new boat plan while keeping the existing boat running, but the poly puts me in hurry up mode. So it is time to close this thread and start a new build thread.
Backing up a bit, 2 years ago I fitted "new" cylinders. 2 of these were weld repaired, new chrome cylinders (#1 & #2) from Jurnigan's, the other 4 were run chrome with yellow tags and certified for aviation use, bought off the internet. I also got 3 more weld repaired, new chrome cylinders from Jurnigan. Ever since putting on the new jugs it had what sounded like a small exhaust leak on either #4 or #6 (the yellow tag one's), but only at idle. That side of the exhaust always sucked in intermittently at idle too. Further, the exhaust port on #4 seemed to have been machined down previously as I had to use several gaskets to shim that cylinder to header connection. At one point it pulled the exhaust studs and I gave her a helicoil job on the boat.
It takes a lot to line up my glasses, back and a headlamp to look at the exhaust ports on the motor, so I just didn't do that when I sunk the helicoil. Here is the result on the #4 cylinder, note the break in from the tap job.
Further, we found that the ID of the exhaust port is larger than the ID of the exhaust gasket. It looks like previous machining to true up the exhaust flange opened the face ID up too much.
The motor ran fine at load, it just did not idle right. Turns out (as usual) that is for a reason. I did pull #2 (Jurnigan) cylinder also, but all appears well with that cylinder. So all I can say is she was stumbling due to failure of the exhaust gasket and pulling in cool air when the valve closed. The #2, 4, 6 bank now has a new header installed and all is good.
As for the heating issues, my conclusion is that I started with good mags and a crappy carb that was running (real) lean. I added electronic ignition with the plugs gapped to maximum and all of the sudden she was knocking bad. Like they say, lean is mean, she was just lean enough to run and the hotter ignition finished her off. Thanks to GMAC76 I have now have two good running carbs.
At the same time as the carb rebuilds, I added CHT's to monitor cylinder temp. The interesting part I learned from that is that the temp measurements I got with an IR gun turned out to be 100 deg or more less than real CHT's. After the carb replacement and with CHT's installed, running the same hard ground as prior, I had no issue with pre-ignition but still saw CHT temps as high as 600 F. But, before (with no CHT's) I was seeing oil temps stabilizing around 210 but now it was running 180.
Beyond that, I switched to cooler plugs, dropped the plug gap from 0.038 to 0.024, tested a fan and tried a shroud. I have also tested dropping timing from 25 to 22 degrees. I now have a motor running below 500 under normal operations and she takes a while to hit 550 under hard running. She will go to 600 if I let her, but we are done with that except for emergencies (1-2 per day...). Oil temp is now hard pressed to reach 180, and only after an extended hard run.
SUMMARY:
A proper carb is #1. The accelerator pump was not even operational in the original unit.
The cooler plugs and less gap are big ticket items, that made at least a 50 degree difference. It has been said on this forum before to run the coolest plugs you can without fouling, my experience backs that up.
The shroud vs. the fan is about equal, they both knocked about 25 to 50 degrees off the operating temp. I am thinking of combining the shroud and fan, or maybe a taller shroud but save that for later.
Dropping timing, with everything else resolved is still an open issue. On my last runs it did not seem to make a difference and even caused some backfires under load. So I switched it to full timing and have not done anything further there.
Time to start a new thread on the Ghost build. Hopefully the weight, friction and airflow improvements show up in even lower CHT readings next hunt season
Thanks for everyone's input and comments, it has all been worth chewing on.

I still think I-10 is the Mason Dixon line.
2013 Mike Stossel Boats, 13' x 7' deck over, IO-540, 74" NGQ less winglets.