So it keeps doing this again. I rode one time and it seemed like it fouled one of the plugs so I ended up throwing a new one in for the time being and it fixed it for awhile.
If you don't get anywhere obvious from looking at the carb side, you should still not rule out the coil.
Put two brand new plugs in. Ride for a while until it starts riding rough again, then cruise around rough for 5 to 10 minutes. Remove plugs to see which one is fouled.
Then put two new plugs in and swap coil wires (yes, you can do this and it will still run fine). Ride until it runs rough and continue for 5 to 10 minutes. remove the plugs and see if the opposite cylinder's plug is now fouled. If so, it is a sign of a bad coil (or wires/terminals). If the same cylinder's plug fouled, then I'd really focus on the carb/fuel supply side of things. If the opposite cylinder's plug is fouled (problem followed the swap) then you still have a problem with your coil/plug wires/terminals.
Good Luck.