If it's firing well on 1&2, but not on 3&4, that suggests to me that the source of spark is NOT the culprit.
Plug wires are NOT going to be a 'no fire' issue, but use solid core wires on magnetos... battery-coil systems use resistor coils or plugs to suppress high frequency oscillations that will shorten the life of the condenser, points, and the machine operator (if his wife's football game is being interfered with by all that ignition noise)
Locating the spark is the issue.
It COULD be the cap... but Here's what I think:
I think that the points are not getting proper operation on the 3/4 cylinder.
I'd be willing to bet that if you took off the cap and rotor, and grabbed that distributor shaft, and wiggle it around, it'll be sloppy in the bushing.
I'll bet that if you pull that distributor out, and either 1) Drop in a known-good or 2) pull it apart, give it a serious rehab, with a new bushing, and possibly (if it's worn) grind the shaft to true, and undersize the bushing to match, and put it back together, it'll be MUCH happier.
The OTHER possibility (and it could be in conjunction with the shaft bushing)... is that the POINT CAM is worn, and you're not getting sufficient lift.
So you ask WHY would it do this when hot... but not cold?
Well... because the OIL that's passing around all those gears is thick when it's cold... and once the oil is warm, it's thinner.
Now, if neither of those prove out, then the next thing I'd do, is get it good and hot, so it's missing... shut it down, and give it a quick compression test on all four.
IS it low on CR on those two? Either there's some valve clearances that need to be reset, OR there's a compression leak. If the oil and coolant are both clean, it's probably just between the cylinders.
How would I determine wether it was an ignition, or a compression circumstance?
I'd start it up, get it running good and warm, AFTERDARK. Once it starts missing on the back two, pop the plug wires off 3&4, and connect them to some spare plugs that're grounded to the side of the block somehow, and look-see if you've got spark on those two. If they're snappin-nasty-hot, then you're dealing with a compression circumstance, not an ignition circumstance. If the spark you see is flaccid, check the diz shaft and point cam.
ONE OTHER THING... is the intake manifold. In order to provide sufficent carb heat for atomization, the intake and exhaust runners share a wall. When cold, this casting will likely be pretty tight, but once warm, if there's a slight crack buried in there, it'll start opening up, and eventually, you'll have enough of a leak, that the mixture on whichever side will lean-out, and you MIGHT even start to get some manifold backfire (if there's sufficient oxygen and fuel to do so)... but when you cool it off, it contracts and seals up again.
Swapping the intake and carb with a known-good will prove that out.
------------- Ten Amendments, Ten Commandments, and one Golden Rule solve most every problem. Citrus hand-cleaner with Pumice does the rest.
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