It could be a combination of wet/saturated air filter, and wet ignition(plug wires etc.)combined. If you were getting voltage leaks because the spark to the plugs was finding new and creative ways to lose energy due to being wet, it'd reduce your speed as well. Having a soaked filter would certainly ruin your day. The filter is a real weak spot. It has the kewel factor, but it is wide open to the elements.
I would think if the Roadie was that weak where wet ignition components was a concern, we'd be seeing it somewhere on here regularly. There are a lot of members, and I'm sure there are plenty who brave the elements to ride in the rain(maybe not, it might just be BMW riders that do that
It's just anecdotal, but I had on old dodge 265 slant six, that required me to carry an extra distributor cap just in case it happened to see a puddle. I don't think the Roadies are anywhere near that bad, because their designed for some exposure.
Get a shower cap for the filter next time as recommended, and make sure all your plug wires are pushed down tight. Water around the outside of the wires, only needs one wet spot near a connection somewhere along its path to offer an alternative path that doesn't include a spark plug.
You might also keep a poncho or something for the bike when it sits in the rain. A little something over the tank and seat area where all the connections are, couldn't hurt. A heavy four hour rain tends to soak alot of things completely.
Check out Rico's "failed horn" thread. That, is wet, and he is running a stock airbox(I'm Pretty sure).