Yeah, I cut out the box.  And the battery box and toolbox for that matter.  If you can fab stuff up yourself, or know someone who can, the options are limitless.  For example, I TIGged up a piece of aluminum tube and end caps to make an electrical housing that sits where a cylindrical oil tank would be on and older bike.  The wiring, ingnition module, and solenoid all fit in there ( a little cramped, I'll admit, but it still fit!).  I'm also going to make a low profile battery tray out of 1/8 steel, and mount the rectifier on that to keep it in the wind.

If you want to go with aftermarket parts, then things will get a little dicey.  There aren't any direct fit replacements that I know of, but you could use the original box to house all the electrical and just remove the battery box.  I'm pretty sure some of the folks on here have fit everything, including the battery, into that space.

If by the "front hole" you mean the hole connected directly to the carb mouth by a rubber tube, which is located directly under the seat, then yes, that can stay open with no troubles.  The air in a stock setup actually flows out of that hole and into the carb, so if you pull the tube connecting the two and mount another filter in between them, then the airbox will basically be dead weight.