I agree with Mazi re Yamaha vs Honda after owning the Yamahas myself (250 and 450). The internals in the Honda Master Cylinder are different and definately provide better stopping power. Externally they look the same. Judging by feel I'd say the Gas Gas already runs the Honda like MC and coupled with the braided lines gives fantastic feel.
There is zero doubt that an over sized rotor will pull the bike up better. More area to grab and more area to cool.
I have used Metal Gear on the Yamaha and seemed to work well.
http://metalgear.com.au/view_model_d...?model_id=2832
Those racediscs are cheap. I wouldn't expect much from them, but at that price what do you have to lose.