Drilling holes - no good! can see where your coming from with the, it does work on some cars/bikes, only problem on the Brutale would be the amount of hot air the engine produces which will not do it any good, you need oxygen, the hotter the air the less oxygen. Unless you can develop a ram air system for the airbox...
1) A BMC free flowing air filter
2) To fine tune you Brutale with Arrow system would be a Power Commander and setup on a dyno.