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Well done Sir. Excellent find and thanks for sharing your find with us!
Kiwi: As soon as the bowl came off the cause of the rich running on cylinder 1 was obvious. The nitrile bung which seals the pilot jet was missing... As I'm the only one working on the bike, mea culpa. What a dick!
In the Mikuni BS the pilot jet draws its fuel from the main jet. Or from an alternative perspective the main jet meters fuel for both the slow (pilot) circuit, AND the high speed (needle/main) circuit.
If the bung is missing, when the fuel starts flowing through the needle jet, it sources it's fuel from the massive unmetered 'bung hole' rather than the main jet.
You were right about the pilot circuit drawing fuel through the main jet. I had "VM" carbs on my mind and should be more careful before I reply.
I also misunderstood the location of the "bungs" as you call them, compromising my advice.
The BS pilot circuit does draw fuel through the main jet, but the main jet does not meter or regulate fuel flow for the pilot circuit, nor the needle jet circuit. Fuel flow in ANY circuit is always regulated by the SMALLEST port or opening in the circuit. At closed or small throttle openings, the pilot jet regulates flow. For the needle jet circuit, the gap, or space between the needle jet and jet needle regulates fuel flow until the jet needle raises high enough inside the needle jet (approximately 3/4 throttle position) that the gap between them becomes larger than the main jet opening and that's when the main jet regulates fuel flow.
With the missing bungs, the open "holes" were not regulating fuel flow because they were not the smallest opening, but they would introduce a secondary flow that would result in a rich mixture.
I'm glad it appears you've sorted the jetting. I've been there with all the thinking, trial and error.
Just hang in there and don't get frustrated. You're not alone.