Well at the risk of start all sorts of hell... the comments that the WRR runs lean can be misleading.
The bike actually runs a bit rich in the stock form at the higher revs and high throttle opening. There is a lean spot a bit off idle which some say leads to a jerky throttle or hesitation.
I am currently running an open air box with a FMF Q4 and no fuel programmer. Before that I was running a open airbox with a modified stock exhaust - the catalytic converter was removed.
While I do have some throttle hesitation right after the bike is started up it is gone once the bike is warmed up - usually about 5 minutes after start.
I have also ran a open airbox with a GSXR 1000 muffler (flows like the FMF but quieter and no repacking required) with a custom program map for my Power Commander 5. The bike made more power in that setup but the power was shifted more to the upper revs and the fuel economy dropped about 10% - usually making more power means burning more fuel. There was good throttle response even when the bike was cold.
After going through all of this and the knowledge I have gained with my bike over 16,000 miles I would probably not mess with the airbox or the exhaust. I would instead change my gearing to something like a 13/47, 13/48 or 14/50, get some decent tires, change the seat, and save my pennies for some suspension work.
Bear in mind this is based on the type of riding I do with my WRR which typically is not a lot of street or wide stretches of desert. Mostly rides around the Southeast US which can feature sand, woods, rocks, and mud.
I have a riding buddy who has a WRR as well. He is running a Q4 with what I consider a better option than removing the flapper valve. He basically has removed the airbox door on the WRR and has it in one of his tool box drawers ready to go back on if he ever needs it. We have ridden a lot of miles together with many many water crossings. No issues with water ingestion and if you really look at the induction system you can see that it would be difficult for water to be ingested during normal riding. If you have ever worked on a KTM you will see that their air boxes are basically open on the side as well.
Removing the door is simple and can be reinstalled just as easily later if you don't like it.