Don't be too quick to tear the engine apart!!!
You have a fouled #1 spark-plug, and a #1 carb with a fuel level problem. Like I said before, and TwoTired mentioned, the "smoke" might actually be fuel vapor. What does it smell like? Also, what was the clear tube level on 2&4 that you claim was "spot on"? It should be about 3mm below the top of the float bowl.
Well that is encouraging, thank you! 3mm below? I was under the impression that it was supposed to be at the gasket level...(thanks for asking). In that case, only carb #3 is set correctly, 2 and 4 too high (gasket height), and as for #1, no idea what is happening there. I'll pull the carbs and check / adjust float levels again (PD41a @12.5mm)
Not sure about the smell - it's not overwhelming whatever it is (I have to get close to the breather or exhaust to smell anything, and even then, it's not clear to me what I'm smelling, if anything).
Have you checked if the vent tubes are not blocked? (had a similar issue recently where I was sure I checked them when I rebuild them, but one was clogged up and it messed with the carb)
I have not. To be sure, on these carbs (PD41a), if I'm not mistaken, the overflow tubes are also the vent tubes (when gas is not flowing through them)? I'll give them a good clean. Otherwise, at the risk of sounding like an a**, I am not sure what you are referring to.
If you have a squirt gun type oil can put 1 or 2 shots in that low cylinder and retest the compression. If it comes up to match the others then it could be bad rings. BUT BEFORE you do that make sure the valve clearance is not too tight. This will tell you where to focus if you do need to pull the engine.
Adjusted valve clearance a couple of months ago (with very little ride time since), but will double check for good measure.
You found a problem with carb over flow with vibration. Fix that. Might be pumping raw fuel into the crankcase past the piston rings. Does your oil smell like gas? Focus on why your carbs failed their tests.
What is overflow with vibration (not literally, that I understand, but why does that happen)? What can I do to fix it? But now that you mention it, the last time I opened the carbs, I had a very light leak from the float housing (pretty sure it was carb #1). Tried different float needles and different orings to no avail. As it was hardly noticeable, and not something easily repairable (or is it?), I left it as is. Maybe it got worse in the meantime....
Regarding the smell of the oil - is that something that should be done when the bike is running, off but warm, cold, or does it not matter? When cold, shoved my nose as close as I could to the oil tank opening, and it does seem to have a hint of a gasoline smell... On the other hand, my sense of smell is nothing to write home about and it may have been just in my head (as in I was "looking" to smell it, so I smelled it). Anyway, it definitely was not neutral in smell (which I would expect from oil).
Did the bike fall over when the forks collapsed?
Nope...