So, after fixing the carb/fuel petcock issue, my concern now is brakes... Maybe I'm just a bit too used to my yzf600r but it seems this fun little bike is a little under powered when it comes to stopping..  any advice on easy upgrades?

The sintered metal HH pads make a noticeable difference.

1  as jack said   better pads
2  better brake line(SS or kevlar...your choice)
3  R6 front end/90-95 GSXR 750 front end
sky is the limit
that krazy german had 15k+ invested in his GS