It depends on your situation. In a nutshell..

Pilot jets handle low speeds
Main jets handle higher speeds

your problem was at higher speeds so a good starting point would be to change the mains first.

I figure youre trying to make one order from newspeedmaster and get everything you need right off the bat to keep the waiting down. Its a pain, but take your carbs apart before you order so you know what your working with.

Theres no hurt in getting a couple mains, the next bigger pilot. and DEFINATELY allen carb screw kit.

Take a look at the screws on the top of your carb. If theyre the stock screws they'll be phillips. You'll want to replace them with the allen screw kit when youre doing the rejet. The stock screws will strip right away and you'll have some major problems at that point.

You can find the same screws at an ace hardware put make sure theyre the same length and Stainless steel.