Amazing setup, nice to see a stroker build,
i too think your running a little too much oil causing the darkening on the piston,
some points i saw was that you could probably try with a higher rpm pipe the homet p6 is good ( i run one too) but for higher rpms you can use a scooter pipe,
by what you have described you have a rich in the mid situation, one way of working around this is a boost bottle designed for the bike in question, some people say they're snake oil but ive found a well designed boost bottle can help with rich in the mid situations.
also have you used this website to see what rpms you are running for you gear/wheelsize ? http://toolbox.martysgarage.info/ seems your spinning around 11.5k RPM's which is great and probably due to your low gearing,
a good test for your engine would probably be to gear it higher maybe 17-42 and see how the bike responds, if it can keep the same rpms that would be topping out around 60mph :O