Free up air
I don't believe you will have trouble with either in the rain.
I cannot tell you which is best. There are lots of bikes out there with both so you should get some reports. I believe you will find with either no big gain is achieved unless you go through the air flow front to rear. More air in, re-jet the carburetor, and open up the exhaust. the change in air with out adjusting fuel mixture will result in little gain and a lean mixture. The numbers I hear from doing all three are about ten to fifteen percent increase of power.
Nothing is free, you will loose mileage, and hear an increase in noise. Both intake and exhaust. I don't think intake noise is a big deal with the 1100. Some bigger bikes it becomes significant. The crouch rockets will still blow you away but you will have the satisfaction of having done it.
Lets hear some first hand reports.