I'm personally planning when I build mine to simply put them into heatshrink. That's how I install other modules like the Super-Chuffer, solve the problem of shorting to anything.
Trying to make it the exact form factor of a 9V battery seems a bit of work. It's as short and as narrow, but the thickness will be close. However, since the battery clip is going to be on a wire, you'll have more flexibility in placing it.
