I already posted about my carbon fiber helicopter boom, for that I decided I'll bite the bullet and do alloy molds. 
I also need a carbon fiber helicopter canopy. Similar shape to a football but a bit bigger and open at the back, I'll attach a pic of one. It will have pretty thin wall thickness, generally they are about a half mm, maybe .6 or .7. So only a couple layers of weave. 
I will be making my own design on fusion 360 and milling the plug on my cnc. The process that makes the most sense to me is milling each plug half (mold will be split down the middle lengthwise, right and left half) out of mdf or foam, spraying it with layers of duratec primer, sand and polish, then attach each plug half to a flat sheet of melamine or some other rigid plastic to create base for mold flanges and proceed to make fiberglass mold halves from that. I would prefer to skip the plug stage and go straight to milling the molds, but it just doesn't seem to work out as well as making fiberglass molds from a plug.  From the female molds I will vacuum bag a carbon fiber wet lay up. 
does this sound like a good plan or is there an easier/better way considering I have a cnc? Another variation would be attaching the 2 plug halves together to make a complete plug before applying duratec,  then split into 2 molds using the method shown in the air box video, but i feel that it will be less work to just attach the 2 halves to flat sheets for making the molds, just need to make sure both sheets are perfectly flat planes. 

I'm with Oekmont - joining two separate halves isn't ideal. I dont see why this cant be laid up as one piece, but perhaps I'm missing something from the pictures. You are infusing it correct? So if youre worried about the opening being too tight to fit your hands in to layup, just lay up each half separately before bolting the mould together? It can be fiddly but it's far from hard.