You are on the right track with your mixture screws. The larger pilot jets could actually require the screws to be turned in even more to be just right. Regarding the hole in the airbox cover, I would cut it exactly as specified in the Holeshot instructions. Dale has worked out the best combination for the B 1200. I installed my kit exactly as specified and it worked wonders. In the late 1980s I had a similar experience with a well developed kit. I bought a Toomy Racing kit for my RZ 350 that included expansion chambers, air filter, jets, etc. First I installed the pipes and jetted them the way the local "experts" advised. The results were good but not great. Then I rejetted exactly as Stuart Toomy has specified in the instructions. The results were spectacular. When you buy a jet kit from someone like Dale Walker, you are not just buying parts, you are buying the development work and dyno time that he used to work out all the details. The details are what make the difference. Good luck.