You mentioned you have to hold the choke to "On" the whole time. Are you releasing it once the bike has run for a minute or two? Once it warms up a bit, the choke should be fully off.
I don't know the quality of the fuel you buy, but 87 octane is all you need for fuel. Unless you are buying your fuel from some fly by night place, I would eliminate the fuel filter all together. I have run mine for close to 36K miles without issue. I add Seafoam to the fuel about every 3 to 4 tank fulls and the carb jets stay very clean.
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