My Raptor has a 12:1 comp 102 mm (686) piston, stage 1 cam, pro flow, yoshi exhuast, and I've got 160\165 in mine and it runs great. No problems at all. I don't have the port work but maybe try smaller jets and see how that works out. Of course I'm running at 5,000 ft as well.

What compression piston are you running? I'm using a mix 50\50 mix of premium and 110 octane fuel. Depending on what compression you've got that could be fouling you up as well.

 

I almost forgot....check your choke plunger. Mine got gummed up once and was stuck open. My Raptor experienced similar symptoms as yours and I didn't discover it until I tore into the carbs.