Never been on a Ninja 650, but my buddy had a SV650 and the low end torque made that quite prone to wheelies. Of course it wasn't strapped, stretched, etc either. Anything she could get some seat time on at this point would help. Having never seen her ride, I would say its your judgement call from here.
A lowered/stretched ZX-6r will not have any wheelie problems w stock gearing. And if the suspension is set up right with a good tire it won't spin off the line, especially since starting out she should leave at idle. The ZX-6 will be trapping a lot more at the big end though, I would guess between 110-120. So thats something to consider.