If it's got vee mounts, stick with vee brakes, you can get a solid setup with them, and you can get good pads. Sounds like it has maguras already though.
Normally on phase bikes the first thing to go is the gears, which is done, and then the rear hub, which you'd want to swap out for a hope pro II.
You could change the stem and bars to ones that suit you better, do this after you've ridden it and got a feel for it, and where it could be improved.