Scooble - I'd be willing to bet that fitting a standard Honda paper air filter will get rid of your issues.

I'm sure it would, but I am assuming that a less restrictive air filter improves the volumetric efficiency of the engine which isn't a bad thing, its just that my jetting isn't suited to the airflow at the moment.
Getting as much air and fuel (mixed in the right proportions) into the engine must be a good thing, however, I am not a big fan of the no airbox setup, as I believe that a large volume of still air is best for engine breathing, so although no airbox offers more air (good), it tends to be more turbulent (bad).
I believe that these 'holes' can be overcome with the right size and combination of jets/needles etc - but I'm not sure where to start as a baseline

My deceased trackbike ran what I think was the RLR setup. No filter, airbox front lopped off with fibreglass ram air intake running over a modded radiator. Breathers all plumbed into the box. Air jets were blocked with short lengths of solid core wire, short stacks all round and small 112 jets. Needles were standard.

It ran like a dog off-load but worked well on the track.