Hey hey, don't you just hate tosser dealers. Bet they'd take more care if it was their money that paid for the bike. Said fact is that most mechanics who actually know thier shit working for themselves, not dealers.
The brake on my 7 is pretty powerful, it will step out bick time if your not very carefull with it. But Kawasaki will have put the spring on for a reason.
PM rob(blackzxr) and swap photos with him(of the bike I mean). He's got a beutiful black new 6r. If you need help changing anything, I'm sure there are a couple of members who cauld help you up there with the assistance of info from Rob.
At the end of the day though, the tossers who changed it in the first place show have get it right. Walk into their shop an hope onto their floor model first. Then ask them to explain. Then explain that you are not spending another cent and that you are a very active and popular members of a huge Kawasaki dedicated club. Lowering can not affect the brakes.
Good luck. Let us know how you go.

It is far better to dare mighty things, to win glorious triumphs, even if chequered with failure, than to take rank with those who neither enjoy much nor suffer much, as they live in grey twilight that knows no victory nor defeat.