On lowering the Ninja 650R - the idea is to cut the seat height first, then rework the rear shock, and then lower the forks if still required. Last thing I want her on is an ill handling sportbike.
Trust me, lowering the 650R is still a giant step in the right direction. My Wife's SV650 is lowered 2" front and rear and it will still out handle my old Warrior that was lifted and had R1 forks put on it any day of the week. It will even out handle my Strom which has the preload cranked to the max.
Lowering a sport bike will still make it handle night and day better than any cruiser on the road today.