First off, OP Gsxr996, welcome to the oRg. I see you joined 2 years ago, but have not been a big poster.
Your comparison of riding two-up on the Busa vs. the ZX14 is interesting. I've been riding with a passenger a lot more lately since we have a foreign exchange student with us this year and I agree with you that the Busa handling is not nearly as good 2-up. Part of that is my passenger who is not experienced riding, but getting better. I can't compare the Busa to the ZX14.
I think some of your experience may just be learning and adapting to the new bike. I bought a new sports car this spring, same model as my old one, but two generations newer. The cars handle very similarly, yet I am still feeling out the edges of the new car after several months of driving it. The new vehicle is better in all respects, but I just am not as comfortable sliding her around like the old car I had driven for 9 years.
Perhaps it's the same with your Busa. You've likely gotten a lot more seat time solo, but not nearly so much with a passenger. Both you and your passenger need time to adapt to your new mount. There are so many small adjustments *we* make when riding, both pilot and passenger, and it takes time to develop the muscle memory. Give it some time and don't keep screwing with the suspension.