Need help fixing Alpha maps

Well I have textures and I have a spaceship. This is exported from a game and I have no idea how to fix a couple things.

First thing, is fixing the alpha with the transparency. There are blocks that are like old minecraft grass, two intersecting planes. I can’t seem to keep the glow while removing the alpha. http://i.imgur.com/7aX38c7.jpg

Second thing, I can’t seem to keep the texture for the things with light and emission. I only get the light color, but I can’t seem to keep the light textures. http://i.imgur.com/laKtNsx.jpg

Blend File (Cycles): https://drive.google.com/open?id=0B0m-o3QpmKFhNVVTZl9MNUNsQzA