That guide roughly agreed with stages in my head.
Stage 1 - Air filter and Slip On. Mainly done to say you did it/make your bike louder. May have minimal hp gains.
Stage 2 - Cam. I would normally stop here (with a good exhaust), you have unlocked all of the cheap and easy potential in this bike.
Stage 3 - Heads. Getting damned expensive, probably well past the point of diminishing returns.
Stage 4 - Not normally done, increased cc's, turbo, nitrous, etc. Normally reliability starts to take a beating here.
At somewhere around Stage 2 or 3, a full exhaust system comes into play. Obviously, for every stage above 1 (and sometimes for 1), fueling/carb may need to be adjusted.
Based on the above, for the most part, each stage is working on a separate part of the engine but if you are planning to push further in the future you need to plan so you don't end up with orphaned parts (eg slipons or a mild cam if you plan on building a fire breather in the near future).
I've had a few stage 3ish mini motors. They sound good and they are lots of fun, but the first grenaded the bottom end. The second is probably down 20+ hp on the first (~100hp 1.3L for the new one), but it is rock solid reliable. I am struggling whether to put the fancy head from the first one on the second to get back most of the lost power (probably).