3&6 missing, stalling when put in gear

My valiant has been a garage queen for 5 months because of this. '68 Valiant with a 225 and auto trans. It was my daily driver for a long time. It's got a reoccurring issue that comes and goes.
First off, some things about my car.
-No choke. I removed it years ago because the mechanism was missing/broken when I first got it. I live in a tropical climate, and usually 3 pumps on the gas pedal starts it on the first crank.
-Remanned carb. It has had this same issue with the original and remanned carb, but also run right on both carbs.
-remanned distributor from a '66 slant six. Found this out while shopping for a new set of points all day. Car ran good when I originally got this dizzy.
-fuel pump and filter are new. This car has always had a plastic fuel cell in the trunk, and it uses an inline clear plastic filter.
-no vacuum leaks I can find. Not on the throttle shaft, base gasket, intake manifold, pcv valve. I've tried capping the vacuum advance and connecting it, no difference.
-Compression reads between 130-140 psi on all cylinders.

Recently I've replaced the cap, rotor, wires, condenser, timing chain and gears and associated gaskets. Timing runs 5* btdc, spot on . I've checked the timing, run it with and without the vacuum advance, checked points gap, and the valves were adjusted about 3 months before it got parked due to the issue it's having.

THE ISSUES:
On cold starts recently, it runs rough, sounding like 4-5 cylinders. If I let it idle for a while, it will eventually smooth out a little. Put it in drive or reverse and it will stall almost immediately when touching the throttle. If I feather the gas, I can get it moving and it becomes much more willing to move once it's rolling. I've checked the accelerator pump, and it puts a nice strong stream into the carb. Carb is spotless inside. Once warmed up and moving, it's got a very occasional cough at cruising speed, but not enough to notice unless you're listening for it.
I throw the timing light on each plug wire, #3 has an occasional pause in spark over 2000 rpms, #6 is firing about half the time. Strange thing is, #6 has ALWAYS run rich as long as I've owned the car. Running good and peppy, or shitty and rough, #6 plug is ALWAYS black.... with multiple tuneups, 2 different distributors, electronic and points. #6 is black.

Anybody got a clue for me what to check next?