Replacing the air box with a pod filter is more straight forward than it looks....remember that underneath all the garbage is just a simple carburetor. The trickier part is deciding how you want to handle the battery and all the electrical boxes, fuse boxes, etc. What's the point of installing a pod air filter if you can't clear everything around it so you can see it?
Using common sense and paying attention to what you're looking at, you can disassemble the stock airbox easily. While you're there I recommend pulling all the smog crap off (this is fully half the garbage down there.) You need to clip the vacuum hose going into the carb and run a screw into it. You may also want to step up a jet or two in the carb, depending on whether you're running an aftermarket exhaust.
Now for the tricky part: Where to put the battery and what to do about all the wiring? I unscrewed all the wiring harnesses so they were floating in the open space, gathered them into a neat group, wire tied them into a a flat, organized mass and mounted them just under the seat. This is about the best option I could find. The battery is tougher because it's a big dumb block. I mounted it to the swingarm just forward of the rear wheel. I bought a louvered chrome battery box cover to dress it up.
One more hint: If you buy a roll of black athletic tape (the type you'd use to wrap a tennis racket or hockey stick) you can wrap all you electrical wires and give it that old skool fabric wire look. $3.
Here are a few pics:
Arranging all the guts
I added a piece of PVC to extend the reach of the pod further into the open space
Comes out pretty invisible if you work the wires correctly