I can understand wanting to open up the center frame work for aesthetic reasons; I did the same thing to my Suzuki Savage. That was just moving the battery, though. Speaking of which, do you plan on moving the battery, too?
If you want to use ammo cans, they aren't really expensive. They are certainly cheaper than ANY saddlebag you can find - including everything on Jafrum. The metal makes them much easier to manipulate and customize, IMHO.
http://www.cheaperthandirt.com/product/ZAA-095Another idea: Take the plate with everything mounted as is, and bolt it to the inboard side of the interior of the ammo can. You could cut slits on that side, and if you're fancy maybe even punch the material out to make a wind deflector type opening. You could get the same effect from cutting larger openings and bolting on a deflector. Just make a nice little metal shelf to slide over your electrical plate and voila! Out of sight, out of mind. Drill a hole at the bottom of the box and route all of your wires through there. Don't forget about your fuses! They NEED to remain accessible.
You wanted an idea, so here you go. I'm curious to see how you go about this.