The good thing about the V and Wee Strom is so much is known about them, many thousands of owners have tried just about everything two or three different ways. BUT ... IMHO, If you could sub an oiled, foam filter for the stock paper one, I would JUMP on that ASAP.

This problem would never happen if the air filter was working 100%. No dirt is supposed to get in there, rods and butterflies should be clean. I took to laying down a small grease bead on sealing edges of my paper filters upon install. REally did help reduce amount of dirt ingress.

On my DL1000 no codes or F.I. things came up after removing secondaries.
Throttle response was actually BETTER right off the bottom and fuel economy was the same. Win Win for me!

It was funny to rev the bike and watch the rods move to "adjust" the secondaries ... with no secondaries there! Yet, everything ran normal!

NOTE: I've no idea if any of this applies to Wee Strom. But like the DL1000, I'm sure it's all been worked out for the Wee by someone on some Wee forum somewhere.

The durability of the DL1000 motor is astounding. Even after ingesting quite a lot of dirt from many many off road rides, my DL1000 engine still showed FULL compression, valves remained in adjustment with NO oil use to speak of at 90,000 miles of very hard use. Yes, the bike had very good maintenance and oil changes but was used FAR harder than most. Very tough bike overall, and looks like WEE is just as tough.