Air. Fuel. Spark....it has to be one of the three.
You've already chosen to NOT source an air box and to run the bike without pods or anything on the intakes (This makes your air/fuel ratio LEAN) just to see if you can get it to run...
You haven't adjusted carbs from stock jetting to compensate for the leanness, so your air/fuel ratio is way off.
...and still you wonder why your bike wont run on all cylinders.
Members here will not continue to assist when you 'wing it' after appropriate suggestions are made.
Sorry, man. I'm out.