Well I am still having the issue with the bike idling only on carbs 1 & 2.
Tonight I turned the mixture screws all the way in on carbs 1 & 2, left 3 & 4 open, turned on the choke and the bike fired right up running on 3 & 4. I let the bike warm up, turned off the choke and the bike actually stayed running, but it only ran for a few seconds before it quit. It runs much better off carbs 1 & 2. I took all of the jet blocks out yesterday and verified that the pilot jets were definitely not plugged up and they were clean.
The only other thing I am leaning toward is a possible electrical issue. I just installed a brand new Odyssey PC 680 about a month ago and with the bike idling at 1000 rpm I am getting 13.05 volts across the terminals which according to the electrical troubleshooting guide here on this site, that is marginal. Could this be causing my issue? The bike definitely runs on all 4 cylinders above the idle circuit. Also, have new COPs installed and I know they are all firing.
So I'm thinking it's something with the charging system or the idle circuits are still plugged on those 2 carbs.