Just remember that if you actually remove material from the inside of the engine it's no longer stock... i.e., it's now an Open class bike.
The inside of the engine has to be left just as it came from the factory. You can change gaskets all you want and play with different base gasket combinations but you can't "modify the metal."
Conversely if you plan to run in the Open class, then port and tune away. Just remember that porting is a pretty exact science. If you don't know what you're doing you'll just end up with an expensive paperweight.
