The skip on idle returned. Replaced the ignition box; no change. Replaced the coil, no change. So, there are spares for road trips. Also have an extra distributor so backups are available for the whole ignition system.
But I believe the problem has been found. I somehow got the rocker screwed down way too far on #5 intake valve. Can NOT imagine how that happened?!?! Could get it too loose if I somehow adjusted it off of base circle but how could I get it way too tight??
Found it with a leak down test. When I shot the header tubes with the remote thermometer, this time #5 was about 200* colder than the others. Pulling #5 plug wire had no effect on idle. Did a compression test and got 125 PSI with the other 7 plugs still installed. Not great but shouldn't affect idle. A leak down test had air hissing into the intake. Pulled the valve cover and discovered the problem. Don't think it did any damage, although it certainly could have. Idle is OK now. Haven't had it on the road yet but if the idle is good I'm sure it'll drive fine.
With that intake valve closing and the bigger air bleeds, the idle mixture screws now behave like they should.

Think I'll drive it a while and check the plugs again before installing larger jets. Or, maybe I'll spring for a dyno pull with sniffer. Have to get the resonators installed before any dyno pull for sure.
The new KYB shocks work great. The soft ride that a big old Lincoln should have is still there but it no longer wallows around. Handles much better on curves. Maybe it won't get bigger sway bars. The take off shocks could have been original. More rust on them than on anything else on the car.
Based on some advice I read, the aux trans cooler was installed bypassing the cooler in the radiator. Advice was to not use the in-radiator cooler with an aux cooler in warm climates. After thinking about it some more, I think that's not a good idea in this case. The cooler is installed behind a hole in the bumper where the fan isn't pulling air thru it. So, when idling in traffic the cooler isn't cooling. The trans didn't act right and may have overheated when stuck for 30 minutes on the loop around Raleigh due to an accident. Gonna put the in-radiator cooler back in the loop.
Happy days are here again!!