First of all go with a pipe and silencer, reeds and a new air filter. That right there will give you a ton of power, don't forget to jet the carbs. If you don't ride a bunch of nasty wet stuff, get an airbox delete kit. With proper jetting, this can add more than you would think.
Then you can take the cylinder off and have it ported, polished and decked and install new domes and high compression pistons, this is what I would call stage two stuff. At this point you may consider upgrading the ignition and clutch as well, you will likely need it. You can also consider larger carburetors here, but may wait until the next stage.
The "third stage" would be upgraded cylinders, such as the cheetah cylinder kit and a stroker crank. By this stage you will need a larger radiator, heavy duty clutch, heavier rods and upgraded ignition.
Don't forget proper jetting with any modification. If you don't jet, even with just a pipe and filter, things can go sour quickly. Also don't forget to use a quality oil with a rather lean oil to fuel ratio, like 40:1. You can go as high as 100:1, but you need a very high quality oil, one that was designed for such a ratio.