I used to have one of those bikes (88R100RS) my first BMW, wish I still had it.
Personally I would leave the stock air box assembly on it, you are basically dealing with a known quantity. The manufacturers put quite a lot of research and design into these parts to make them work well. You can insert and turn the key, fire up the engine and ride away with out fiddling with it. If you have a problem you know basically that stock parts will fix it.
If you go down the slippery slope of modifications, many times every little hiccup becomes a pain in the ass to find and repair. Do a little search of carb replacement and jetting, there have bee a lot of those recently.
I have been there and got the T-shirt, I like to keep them basically stock and just ride them. If it becomes a pain in the ass, you will be less likely to ride it.
If you want a performance bike, buy a performance bike.
It is ultimately your bike, ride it and enjoy it.