1) Your textures size should be a power of 2. It doesn't have to be square, but each length must be a power of 2.

2) I'd recommend just using 24 bit textures. Don't waste your time with 256 & 8 bit colors...

3) Alpha channel just tells how transparent a certain part of an image is. An image (with alpha) has 4 channels [R G B A]. The alpha channel is just like the other [RGB] channels, but instead of color, its transparency. Google it... or wikipedia...

4) MDL mapping just creates simple two-sided UV maps. MDL2 mapping allows greater flexibility with any different angle. These are just ways of creating UV maps, and they can be combined.