Well, last time I heard "dead spot in the carb", it cost me a carb rebuild, valve job, tune up -- had to borrow money to pay for it, and still misdiagnosed -- turned out to be a collapsed fuel line. That was in 1973 ('69 Olds). Moral is, first look for the simple solution.
got some "not sures" about your narrative:
not sure about partially clogged idle jets -- or more to the point, not clear how you would determine there is only a partial blockage. Must be making an inference. In terms of function, the jet is either open and working, or it isn't. But maybe found some general nastiness when the expansion plugs were out, suspected to cause issues. And guess it's possible the idle jet may be getting some periodic blockage, giving uneven (unpredictable) operation.
Also, not sure what you are seeing with a clean top plug. Could mean that no fuel is getting from the carb to the cylinder, so no carbon (said you could see fuel in the carb -- guess I'm not sure what you mean there either. Gas in the bottom of the throat when you look in?) Clean plug, compared to carbon on others, could also mean that the plug is getting washed -- that water is getting in there (poss. leaking gasket, like you mention).
Might spray some fuel mix in through the top plug hole, and then see if you can get it to pop. Make sure you have spark on top along with good compression (two givens.) If no spark, will obviously address that. If low compression compared to the other two, first try replacing the head gasket.
A guess from here -- cylinder is probably not getting gas for throttle up, and might concentrate on the h.s. jet. I would try first to clean the H.S. jet in the top carb. Carefully run a small diameter wire through it if you can, and flush with carb spray. Ain't supposed to use a probe, but may be the best solution to a nasty clog. .054 is about the size of a paper clip wire, isn't it? (so not all that delicate, although brass.) If it's seriously varnished up, spraying alone isn't likely to do it, nor soaking for that matter. What did it look like?
You discussed some of this over in the props forum, and would help if you summarize what you did or didn't do to address running issues: Compression, ignition, carbs, fuel pump, fuel mix, tank(s), dropped cyl test. Some of the issues were probably addressed.
