The stock air filter on the 1100 is not the restricting part of the intake system. Switching to a K&N does nothing for the motor. And many people say the K&N does not filter as well as the stock unit. So, you might just save your money.
The real restriction to the 1100 is the size of the air intake at the back of the air filter housing. Making some holes around the side of the housing will take care of that but if your bike is like most 1100's, it will hardly run after that mod. A serious amount of rejetting is required if you fool with the air box. And to get the jetting right again requires access to a dyno and numerous runs to sort it all out.
The exhaust system on the 1100 isn't really very restrictive. And due to the nature and tuning of the intake system, changes there also do nothing for the power curve. And I've yet to hear an aftermarket system that wasn't too loud for my taste.
But, there are some things you can do. First, make sure that the carbs are in perfect condition and synced properly. You'd be amazed what this can do if they are off a bit. Second, rejet just enough to take care of the EPA mandated leanness. On my 92 ABS ridden here in the Silicon Valley, this meant going up one size on the slow speed jet from a #38 to a #40, raising the stock needles .5mm, going up one size on the mains from a #125 to a #128, and turning the mix screws out to 2.5 to 2.75 turns total. The result was an improvement in low and midrange response (crisper throttle response) and an overall increase in torque and HP of about 3 to 5. Nothing to really write home about, but nice. The main difference was the bike is now more responsive and has a bit more grunt, right now.
The last thing I did was to eliminate both the PAIR system and the fuel vapor recover system. Both these smog systems operate and run by vacuum taken off the intake ports and the carbs themselves. There are two intake ports where vacuum taps are located and 5 spots on the 4 carbs. It's my belief that these vacuum systems have a tendency to soften up the carb response and when they are removed, things get crisper and more precise.