Put them back in, opposite cylinders. Dark one is normal colour and no carbon buildup. Pull off the plug wire on the darkened plug side and see if it still runs. I suspect coil problems on the like new side.
So much wasted time here on a slow leak. Do the Hanes Test. Take your wifes or Girlfriends nylons and wipe it around the inside of the tire.
If it does not catch on anything you're good. If it does remove the foreign object. Then buy and install a tube. Get help if you have not done this...
Your description indicates that it is running in a lean condition. Try giving it a small bit of Choke. If that cures it, then you need a carb /cleanout/rebuild, perhaps opening up the main jet beneath the Emulsion Tube a tiny bit. Remove hose at filter and Run some Carb Cleaner directly into...