Drilling the carb is a piece of cake. Don't even give that a second thought.
I posted earlier that thiers a mod review for the lakota.
Go to the bottom of this page, click on atv connection magazine, then go to the top right search box and type in lakota.
Thiers five steps to what they did and what they found. I would print it like I did because it disappears for long periods of time.
Now after you read it "I WOULD LIKE EVERY ONE WHO READS THIS TO UNDERSTAND" these guys have no idea what thier talking about when it comes to jetting the carb.
1)Don't ever mix any kind of jet with a dyno-jet kit, exspecialy the yamaha 136.4 or what ever they said it was. My reasoning is, dyno-jet has thier own index and flow sizing of thier jets. Meaning they are not even close to the one they refur to!
2)The reference to the stalk jet being a #140 and the biggest main for the jet kit have absolutely nothing to do with one another.
3) They didn't find the main to be lean until they raised the c-clip on the needle. They did this backwards. Lower your main first then if your a little rich raise the c-clip.
They were lost here if they thought it through they would have found a #134 that is a little lean could have been fatten up by putting the c-clip on the third slot or taking a couple of disc out of thier TUNABLE exhaust system.

My suggestion would be, put the #138 main, c-clip on the third slot, and all twelve disc in the megaphone. Ride the bike for as long is you can stand it. it will be much quicker.
Now you know what it feels like. It's probably fat, your probably back firing coming off throttle.
Turn the air mixture screw out one more turn, this will take care of that back firing. Drop the main to a #134 (if your rich), if the #134 proves to be lean, remove two disc out of the megaphone.
Were to go from here, I don't know yet. I'm going to do some experimenting when I get home this week and will have to get back to you.
But don't worry, as you can see I love to run off about the lakota and post just about every thing.