Stage I is upgraded air cleaner, exhaust and added fuel.
Stage II is Stage I plus cams. Lots of guys add a BB kit at this point. (and the moco stage II kit does just that)
Stage III is the above two, plus head work
Stage IV is anything you want it to be.
At the dealership, Stage I generally is a SE air cleaner or equivalent, free flowing slip ons, and a stage I ECM download. Instead of the download, you could substitute a Power Commander, FuelPak, SEST or similar method for adding fuel. Back when it was all carbureted bikes, the fuel part was handled by re-jetting.