Ok, first, on your box call, you should never sand on the rails, any at all will cause you to lose certain aspects that were built into the box to make it work...two, you can however lightly sand on the underside of the paddle, if you feel you aren't getting the grip and friction you need to run it right, BUT...DO NOT....use too much pressure just enough to see a little dust, that is all, also sand with the grain, not across the grain.
Three pot call surfaces in different materials do indeed make different sound, when it comes to pitch and rasp, but the majority of the sound produced by a pot call is in the striker and the internals of the pot itself. Thinner pots tend to bring the pitch up, where thicker pots, (if properly fitted with the correct pedestal height) will tend to lower the pitch initially, then the thickness of the striking surface and the density of the striking surface will make for different resonation changes within the pot. The strikers play a major roll, the more dense the wood the higher the range, the lower the density of the wood the softer the run, length of the striker will also make a difference, as you are working with friction and grip in order to create the sound.
Glass can be reconditioned with the proper sandpaper, any sandpaper that is harder then glass will do, but hang around the 120 - 150 grit, you can also recondition glass with a diamond dusted dremel wheel, NEVER try to recondition a ceramic surface, it is hard, harder then anything you can use to do so, just clean it with an alcohol pad, if you must recondition it, use a diamond dusted wheel.
You can definitely over do any kind of conditioning on the pot surfaces and the striker, just a light sanding in one direction on the tip of your strikers should be plenty, until they get dirty again or filled from the slate or something. I take the striker and rotate it in one hand while lightly running the sand paper across the tip with the other to insure a well rounded tip.
