hi mik - gretings to you too!
have a look at this link, as it explains the mod roger has told you about.
http://www.ablett.jp/bikes/vtr/air_box_lid.htm
this guy didnt go all the way with the jetting and didnt get the results he expected, but when i took my bike here for a fuelling run
http://www.junction-33.com/ (next door unit to roger's place) the operator (andy) told me he does all the dyno work for roger and they have done a lot with the airbox mod, with massive gains to be had.
regarding the jetting, he didnt give any specific jetting sizes but said it requires 'extensive modding to a stage 2 dyno kit' and a bmc race filter (which i have)
i take from this he uses bigger pilots, different nedles and larger main jets.
as said elsewhere, dont fit the lighter springs from the stage 2 kit though as it messes up the lift on the diaphragm & fks up the mix)
i think it will be worth you speaking further with roger & andy at the dyno centre about this.
all his dyno runs are saved on computer so im sure he will pull a few moriwaki vtr bikes for you and see what jetting was used - like roger he is a very helpfull guy, plus i'd imagine this time of year he's fairly quiet workwise.
one thing though, when i had the over-rich issues with mine i ran it on trial without the airbox lid & just gaffer taped the filter on and the noise is bloody awfull lol, louder than the art cans i was running.
i decided instead to mod an airbox to leave just the velocity stack mounts and cut them down to leave a 48mm tube sticking out, then mount a pair of k&n bellmouth filters directly to the carbs, attached to the tubes, essentially doing away with the entire airbox.
good luck with this mik - obviously i would be interested in what gains you get.