Hey Ferris. Unfortunately the best way is to make a new wiring harness once you locate all your components exactly where you want them. I have some time investaging this and it's the only real option. If your gonna do it, do it right.
But to answer some of your questions, yes the fuse boxes will fit between the engine and frame. But keep in mind that it is all one harness. All your wires for your controls are in it too. If you took all the electronics and pulled them through and mounted them under your airbox you would have to extend some of the wires back out to your controls, front lights etc. anyway. You would end up with a giant lump of folded back wire harness where you have to bend it back ( right next to the plastic harness cover and sandwiched between the frame and cylinder head ). It isn't advisable to attempt it that way as you will have reliability issues and melted wires.
Your gonna need a manual with wiring diagram, a soldering iron and some patience to do a professional job. Make a new harness using your existing connectors. Solder, shrink wrap, cold wrap. I have some pics of my harness in my build. Click my forum name.
Good luck with it!