I've got a stock exhaust off my wife's 09 fz6r you can have if you want. You'd just have to pay shipping cost. FWIW, she has the 2 brothers header and can, controlled by a Juicebox, runs great.
We put new oem rotors on my wife 6r once we figured out where the clicking sound was coming from, the new rotors do the same thing, so I'm guessing its normal.
It's possible what you're hearing could be the small amount of play between the brake rotors and the carriers. While holding the front brake pump the forks up and down while watching at the bobbins between the rotors and carriers for movement.
When you're doing this (holding brk's/pumping forks) watch the bobbins between the brake disk and carrier and you might see small movement. I believe this is what you're feeling and hearing.
Along with what FastFreddy suggests.
I found what looks to be a pretty good howto but on a different bike. It should serve as a pretty good guideline. I suggest taking the forks off the bike.
http://gstwins.com/gsboard/index.php?topic=59261.0
I put these up for sale a bit ago... Make an offer, most likely will let them go fairly cheap.
http://www.600cc.org/forum/f34/kawasaki-ninja-zx10r-mirrors-blk-31168/