The reason you get floppy sounds and such when you tune down to A on your guitar is that the tension of the string isn't great enough to limit the field of vibration for the strings. This causes the strings to buzz against the neck, and also keeps them from being in the proper place for the pickups to pick up the sound.

If you want to tune this low and have decent tone, buy bigger strings. I tune down a whole step in standard tuning DCGFAD, and use 11 guage strings. Considering A is much lower than D, i'd suggest using the heaviest strings you can find, 13 guage. This will also require setting up your guitar differently, possibly having to recut the nut slots, and certainly adjusting the relief of the truss rod.

About the Tom Morello noise, the noise you get when you unplug your guitar while the amp is on, thats what it is, and the wah/whammy pedals manipulate the textures it has. Also, this is terrible for your speakers, and is often the cause of extreme wear on the speakers which leads to frying the buggers. Not a good idea at high volumes. And if you use tube amps, don't do this unless you can afford to fix gear when you damage it. Too bad, it's a fun noise.

Atomic