Hi Chad, if you have raced as much as you say you have you will know what little changes in rake and trail and swingarm length do to handling, not to mention a swing arm that looks to be 6 to 8 inches longer. I have 43mm Gixxer forks and a gixxer 1100 swing arm but i have had the monoshock section removed and the arm shortened to get the arm as close to stock specs as possible and am also having billet triple clamps made to get the trail in a better set of numbers. Another forum member here has a friend that has done the modern front end swap and has trouble with the bike wanting to fall into corners because the trail is all wrong. I know its done regularly the way you are doing it but in my experience, most people wouldn't have a clue about what is actually a good handling bike.
You can change the triple clamp offset but not as much as the modern bikes and a slightly longer swing arm will improve stability but a much longer arm and shorter triple clamp offset won't give you a modern handling bike.