Stage I - Intake, exhaust and tuner (custom tune is best).
Stage II - Same as above plus cams, pushrods and lifters (wouldn't hurt to upgrade your clutch too).
Stage III - Same as above plus pistons and cylinders (big-bore kit).
Stage IV - Same as above plus better flowing heads and usually bigger throttle body and injectors.
There can be some variations to some of the stages like also upgrading oil pump and cam plate with Stage II. If you're going as far as Stage III or IV you would be foolish if you didn't upgrade your crank and bearings or at least get the stocker plugged and welded. Once you do that you can then go to gear drive cams eliminating the cam chains/tensioners which can wreak havoc on your engine if you don't catch them in time. You better have some deep pockets for III and IV. I think some guys are crazy what they dump into these bikes, but hey ... it's your $ do as you like if you can afford it. You can make a Harley pretty reliable and fast if you spend enough. Personally, if I wanted to go fast it wouldn't be a HD ... I traded in a bike with double the hp I have now, but I traded some performance and speed for comfort instead.
If you're going Stage IV, you might as well go the whole nine mile and throw a power adder in the mix too ... nitrous, blower or turbo and convert to chain final drive depending on how far you take it.