Here's how I look at stage I. It's just my opinion, which might be diffferent than someone else's.
Stage I is kind of an interchangeable term. There's a stage I air cleaner, a stage I download, and a stage I upgrade, which generally entails air cleaner, exhaust, and fuel upgrades. Back when we ran carbureted bikes, a stage I fuel upgrade involved re-jetting. A "stage I" bike would include all three.
The stage I download apparantly only raises the rev limiter. But on O2 sensor equipped bikes in closed loop, the ECM will adapt for air cleaner and mufflers, and add fuel. Of course, it's only adding enough fuel to get the bike back to the AFR set by the factory, which is too lean for most of us. Still and all, if you've gone to a free flowing air cleaner, exhaust and the ECM is adding fuel, it's still considered a full stage I upgrade.
In order to address the heat problem, and get the bike running properly, you need to add even more fuel. That's generally done with a fuel management device, such as a Power Commander, fuelpak, SERT, etc.
Lots of guys consider a stage I upgrade with fuel management upgrades to be the minimum upgrade necessary to get the bike running properly.