Messing with the airbox might be a paint, read this, is not exactly about what you want to do but gives you an idea of what you will have to do to change the airbox
http://www.hondatwins.net/forums/63-fuel-supply-carburation/23714-cb400-cv-carbs-pods-how-make-them-work.html
So if you want to convert to signle carb you will have to fab some stuff and a lot of try and error will be involved, this means you will put some time into the machine, so why not trying an efi conversion? you are not rebuilding a bike so I assume you are not concerned about authenticity, I looked into efi conversion but it was too time consuming for me, I wasn't willing to figure out a way to make an efi fit into the frame, but you don't have a frame to fit into.
Ecotrons has a "plug and play" kit that might be interesting even if on the expensive side, and I am not an expert since you can't find many in italy but there is something called microsquirt that should be cheaper since it's only the ecu and you can get the trhottle body injector fuel pump ecc ecc from a scrapyard for cheaper than the ecotrons kit
400cc to 800cc Small Engine Fuel Injection Kit
Also, it comes down to how much you want to spend on the buggy but the efi opens up the opportunity for fine tuning at every rpm and maybe a tubro? you can find some for cheap online or at a scrapyard and might be something fun to add.
I think the best place for the build thread should be the "off topic" section or maybe a in the "project logs"
Here is another similar thread might be interesting for you
http://www.hondatwins.net/forums/63-fuel-supply-carburation/29309-2-1-carb-conversion-2.html