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Looks like a carb setup issue to me.Running way too rich.Are you running the standard airbox or pods?Had it on mine a couple of times until run in.Once was a stuck float valve,another a blocked idle jet and the other time was because the plugs soot up and won't spark through the carbon buildup.Could also be plug caps or coils.Also at only 350 miles it's not yet run in. Needs 500 - 750 miles for everything to be settled in properly.Once at 750 miles make sure you do an oil change.
As you've got commonality with ignition on 2 and 3, as you point out, I'd look at that to eliminate it first of all and before you chase carburation to any degree. This is partly mirrored in the recent post by RGP on his restored 750 with a spark drop out causing very similar effects, worth a read through to see discussion.Also, a quick check up the carb throats to make sure the choke flaps are being fully removed from airflow when retracted.
Here you go.Hope it's all yours is .Good luckhttp://www.sohc.co.uk/index.php/topic,13165.0.html
Check your points as well as they are common on 2 and 3, 1 and 4.