Check your new battery voltage. If it isn't being charged, you have a charging issue. And low voltage affects spark. Unlikely to be stator, unless attacked with axe, 44 mag, or asphalt impact.
The plugs are easily removed with the stock spark plug socket from the supplied tool kit. Honda sells them if you lost it. They have reduced upper diameter to clear the features in the 550 plug well.
Sooty plugs can fail to fire. Which would be a fuel delivery issue. Also possibly a gas cap venting issue, causing fuel starvation.
State the modifications for your bike which make it different than stock.
Cheers,