Jordan, you are crazy. But this idea is not the reason.
Mount your battery (yep, small expensive units work great) on the swing arm pivot rod. Build a small retaining bracket to fit. This will minimize the exposure and you won't need a great deal of flexibility in the length of the battery leads. In fact, its awfully darn close to stock position.
I'd be skeptical if there were sufficient room above the carbs, but under the backbone to mount a "tray". Especially since you're running Mikunis on this build, no? Don is dead right, keep the Reg/Rec in the open. I've given thought to mounting it where the horn normally would be...? Fresh air abounds, "hidden" from direct view, and proximal to major electrics. (Think short wiring harnesses).
That leaves you with only need a solenoid, fuses and relays. I know you're tight on dough, BUT, a MotoGadget m-unit is your answer. A device (see pic) that small has EVERYTHING inside it. Yep, its $400, but hey, with all the Wedding $$$$ heading your way, might be worth an advance on the expenditure
As for the seat hoop, if you're planning on 2-up, keep the triangular brace from stock. You could remove the passenger rear peg gussets, and use Devin's new relocation bracket? Then the only thing you need to consider is mods to the subframe hoop for the seat.
Crop it beyond the shock mount, buy a new pre-made unit, and have a good welder TIG it in. Easy-squeezy. Also insures you can mount rear indicators, tail light, license plate, etc...
As for a brace, I'd encourage you to think about installing a cross brace between the rear uprights of the engine cage, horizontally. Put in between the hangars bolts, and weld it in. Also, have someone re-weld the slip-fit riveted seams on the front of the cage where the head stock meets.
