I've got the filters in, now what do I do with the battery?
Drill two holes through the bottom of the rubber 'sheath' that the battery sits in, then use the two bolts that held the rear part of the airbox to the bike to bolt it down; it may not seem like a very sturdy method, but I've had mine like this for months with no trouble. Some thin washers can be used to improve stability.
If you have a '94 or earlier model, then you don't have the sealed-type battery and rubber sheath, you have the larger, maintenance-type battery that sits directly in the box. In this case, you can cut the rear part of the airbox off with a dremel; works just as well, just not quite as clean a job. Or, you might be able to more easily build a small cage for it out of aluminum brackets or something you can dig up at the lumber yard.