OK,
I had the same problems in my 2000 hayabusa and after many frequent visits to my mechanic we found the solution!!
The first thing to check are the ignition sparks. An experienced technician can tell from there if the bike is reach or poor on fuel.
My bike was poor on fuel and this was causing the cut offs.
We have cleaned and changed all fuel filters from fuel pump and fuel regulator and although in really bad condition this did not solve the problem.
We have increased idle, tuned TPS, checked the stand and everything possible but again we did not solve the problem - bike was cutting off big time.
We have installed a power commander in order to make the fuel reacher (due to open exhaust cans and air filters) but again bike was still cutting out!!!
I was really starting to get disapointed at this point and thinking of selling my beloved bike but then...
We changed both fuel hoses (the primary and the return one) and BINGO!!!!!!
Bike stopped cutting out!!!!!!!!!!!!!!!!!!!
It seems that fuel hoses after some years take a bad shape that blocks fuel making the bike to starv and cut out.
I think the ones I got from Suzuki are tougher and wider (kind of an improvement)
My Busa now runs faster than ever !!!!!!!!!!