2001 zx-6r.... bike idols great and takes off great....after a few minutes bike cuts out...acts like it is getting no fuel...idol for a minute then takes off fine again... have replaced fuel pump...pick up coil...CDI Box..checked to make sure cabs are filling up with gas...they are....stuck on what could be happening here...

when you drilled out the pilot jet you destroyed it. Even if you have jewelers bits they are to big. One drill bit size is 6 to 10 jet sizes. Replace the pilot jets, you are running WAYYYYY to rich at idle.

If condensation in the gas tank makes it into the carbs, the float bowls will trap the water. Too much water and the bike will act as you have described. Drain the carb float bowls. With a little luck you will be back on the road.

Check your in line fuel filter as you may have gunk settled in the lower part of the filter. When you accelerate, the gunk gets pushed toward the outlet of the fuel filter blocking fuel flow. When you let the car sit for a few minutes the junk settles out and allows some fuel to flow.

Has the bike been setting up over winter or for a length of time over a couple weeks, with gas in the gas in the tank? If so, the ethanol additive to gas has caused the fuel to gum up and block carb jets and passages. My recommendation, if setting up is the case is to put a can of SeaFoam in the fuel tank, shake the bike back and forth to mix the fuel and SeaFoam. Start the bike and run at high idle for a few minutes. Shut it down and let set a couple hours and start and run at high idle again. Repeat this several times trying to accelerate. If it's a gum problem, it should clean itself up with one can of SeaFoam. If it doesn't, it could be an adjustment problem, or the carbs will need a manual cleaning.

Let the bike sit for a bit, try and restart it first. This sounds like you just flooded it. Post again if the problem persists and I can assist you with some further actions.

time to clean / rebuild the carburetors

a few things to look at....make sure the fuel pump is working ,is the fuel in the filter ,check choke/cold start is not sticking and not choking the bike,

this is very rare. if the engine kill switch is in the same grip, check it , it may be shorting/ loose/ defective. only other possible thing is the starter relay switch

Faulty Injectors...