Could be dumping to much in and not burning correctly... If you have good spark. Good compression. Like you stated. You only have 4 steps back to go. Reeds, boots, carb, air filter..
Take reed cage out, look threw them and if u can see light around flaps get a new set.. Carbon fiber last longer.
Make sure carb boots are sealed!
Look in HQfourms and take a lesson on jetting to your area specs.
Clean that air box bro, dont over oil a K&N!!!!! ****DONT OVER OIL!!**** (if you take lid off make sure to jet her fat, leave her lean and she'll blow a load)
Oh watch that cross over tube on carbs it still gets me time to time..
But make sure you get your leak down test done.. °good luck°