I'd hit up the mods in this order. Timing advance, Pipe, Port, Carb, Reeds, Head. I'd keep the flywheel stock(because im fat). That additional torque when shifting through the gears is nice. It has a lot more inertia, there for it will keep your rpms higher when you shift. It does take a little longer to rev up.
The timing advance can be done for free if your handy with tools. It can yield a couple of HP.
What type of riding to you like to do? trail? mx? dunes? drag? flat track? demolishing derby?