The main jet will not be giving you any problems until you get above 3/4, throttle, it has no say in the mix until then, that is why a too big main jet is recommended, to avoid the chance of a full throttle melt down.
The problem is either in the pilot circuit or the fuel enrichment circuit.( choke )
Needing the air screw so many turns out points at a pilot jet that is too large, or a float level that allows too much fuel into the carby.
Does the carby seep fuel at all?
The large issue of smoke is possibly a build up of oil in the header pipe being burnt off, and of course a richer than optimum mixture at idle will compound the matter.
It doesn't over flow and as far as I remember it has a stock pilot. I took the pipe off and tilted the quad to check if the oil injection had caused the bottom end to fill with oil, it happened before.
I'm going to take the carb apart tonight and give it a througoh cleaning. I noticed the vent tubes are missing, would that cause a problem?