I just skimmed, so I'm not sure if I figured out your problem or not... If you are trying to make a material transparent and it has a texture linked to the transparency channel, then it will only become as transparent as the texture will allow it. I've wished that transparency values could go beyond 1.00, but at 1.00, any areas of your texture (alpha) that aren't black will always be visible.

I did not know this until last night, but it's apparently possible to use the blend node to transition your texture to another pure black image over a range of frames. Using this technique on the textured parts should let you turn them completely invisible.