Just for people who are reading this years later....
FZ1N 2006. PC5(whittlebeast Averaged and smooth stage 3), Airbox mod, K&N filter, Micron GP slipon, Cat Gutted, AIS blanked, Files mod (40mm), O2 delete, FCE diode mod, 40,000kms on the clock.
Today I did the 4 diode mod that zady5 has laid out for us. I know an ECU flash is the best but I cant spend $700 on a $3500 bike... (5 days old to me)
I had a few "experts" have a ride of my FZ1N and they all said that's the worst throttle snatch/hesitation they have ever seen. (To the point that the bike is unsafe) I was mostly advised that the PowerCommander 5 might be the issue or one of the other mods and to put it all back to factory.. So I tried that and it was still there right between 4000-6000 rpm on the gear change or if you off then on the throttle.
So I put the bike back how it come to me, then did the 4 x 1n4007 diodes.. and wow what a difference... Shifts gears so much smoother without the huge jerking action.. felt like a completely different bike.. $0.98AUD...
Then I thought, hey. Ill try the flies mod.. Pulled them out, made up a jig to hold them in the lathe. Took them down to 40mm, I know other people go down to 36-38.. Just erring on the side of caution.
AGAIN another wow moment... The low down pull has almost doubled, (butt dyno

) 6th gear doing 60km, add 1/10th throttle and you can fell it instantly pulling...
Thanks for the info guys. Has made my new (old) bike a banger..