So I've did rebuild yesterday. Long story short

Scott - You should stop giving people advice to rebuild their calipers

My bike stopped slowing down when off-throttle after rebuild

First turn was kind of scary as I've approached it normally but bike just flew over it

I was not able to get 4 after rebuild but I came to something like 2.5 - 3 (from 0.75-1). So there is huge improvement. Why it's not full 4 revs ? I don't know. Maybe my brakepads are different (causing little more drag than others) or maybe rotor is little wrapped (riding longer time with dragging pads could cause it, although I don't feel pumping on lever when braking).
Back to work - It was kind of pain in ass. When it comes to working on bike I'm very careful and pedantic so I might overdid in some places. Also fact 08 FZ6 have monoblock calipers makes it tight to work on as you can't separate them any way.
While getting first piston is easy then removing second is harder as you have to block passage somehow. If you do it with your hand you can hurt yourself. I couldn't find any better way so instead pushing out with compressed air I've used high pressure bicycle pump.
I had problem with removing old seals without destroying them. I've tried tooth pick, kind of plastic rod. Nothing worked. I had to grab my wood carving chisel set, punch into rubber and pry it out (making sure chisel won't touch anything else as it have all sides sharp like razor.
I've lubed seals and pistons with brake fluid and put it on.
It wasn't hard, but tedious and making sure everything works as it should and there was no mistakes took time.
Now I have to only re-bleed brakes as brake lever is much softer than it was before but it might be also related to pistons moving back to caliper body requiring more lever travel to put pads in touch with rotor. Braking power is very good just travel and feedback feels different.
Again Thank you everybody for guiding me through this adventure
