Check voltage to your coils with the bike not running. Put a positive lead from a multimeter set to 1x VDC scale on the lug on your coil where the yellow/red wire connects and the other multimeter lead on the frame. Then switch the power on via the key. Check both coils. If you have less than ~12.4 VDC then the problem is poor power supply to the coils.
The smoothbores present some tuning problem; especially with no airbox/air filters. you didn't mention compression or cams but if you have a bored out engine, and no air filter, then you could be up near #130 main jet I suspect. You will have to ask someone who has more experience with performance mods, like Jeff Saunders, on what main jet. The pilot system will also be tough... the pilot system tuning is complicated (over complicated) by the adjustability in the smoothbores. The little holes in the tips of the air screws are the problem. I would buy a NEW set of air screws and fill them in with JB Weld and adjust the idle. Otherwise about a #20 or #22.5 pilot would be OK depending on which slide cutaway you have. The Suzuki variation of the 29s used much larger cutaways which means a lot more air at idle and much larger pilot jets are needed.
This is USUALLY where fouling comes from using 29s. Find out which pilot jet you have, which slide cutaway and then buy a second set of air screws and experiment.
With your set up, honestly, I think doing the main jet plug chop to determine the main jet, then doing some roll ons to set up the clip on your jet needles and then working out the pilot circuit as I already mentioned would be the way to go... the burn on your plugs doens't mean much as the bike may be right in one or two areas but rich in the third and you might be complicating the problems with poorly powered coils.