I think all these problems might be linked. 2 and 3 run of the same coil, so if one isn't getting spark the other probably isn't either, and they'd both be getting fouled...and if you'd adjusted the idle to cope with it running on only two cylinders then you'd get the idle speed problem you started out with. I know this because it happened early on in the Z650 project before I set the dwell on the points properly, and I'm also looking for similar (but not as bad) problems with sooty plugs on 1 and 4 at the moment.
Does your bike have points or electronic ignition? Either way I reckon you need to check the wiring again, including all the connections, because at least part of your problem sounds electrical to me.