Start with the easy stuff... fuel, air and spark.
Hopefully the spark plugs will give you an indication of whats going on...if I had to place a bet I would put money on it being fuel starvation.
So... tank breather, fuel filter on the tap and carburettor bank, open up the carb bowls and inspect.

If I read right the bike seems to run better with the choke applied, so maybe fuel.

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Good Luck!