To reply to your post Ed, I have blanked off the air filter hole as it's placed downstream of the filter element and any air and dirt that gets in there goes straight to the engine unfiltered. Just found a suitable bung and fitted it.
After my failure to improve things by dumping the airbox, I did try to run the bike without the airbox lid with no improvement, but I have heard about the compromise solution of drilling the holes in the filter box lid, and in fact have obtained some various sizes of blanking plugs in case I do it and it doesn't work.
So far I haven't had the courage to do so...What size holes did you use?. Do you cover those holes when washing the bike to stop water getting to the filter element?

Aha, I hadn't thought of the downstream of the filter part - I blanked it off this morning by reconnecting a a short length of the original tubing, which I gaffer taped closed. Regarding the holes in the airbox lid, I drilled 3 as there were 3 natural moulding circles on the inside which I used as a guide.No real science, it just seemed neat at the time.I figured that if it caused issues, I would just tape over the holes.Now that CrazyCarl has brought up the interesting issue of sound resonance, I don't know whether it was a good idea or not! But on a similar note, if it was that critical , then surely the removal of the emmisions tube would have also had an effect, adverse or otherwise? I might tape up the holes anyway as an experiment, although I must say that performance wise the end can has made a big improvement - accelaertion up to 60mph is much better.Above that, its the same old story of headwinds and gradients, 75mph still being the most I have got. Speaking of which, is this the sort of top end performance other people have been getting from the Quinqi 200? And in 1st to 4th it revs round to 9,000, but in 5th won't rev higher than 7,500, is this normal?