What I found is that I am not getting 12v to the fuel pump fuse. Does this fuse only show 12v when the engine is cranking or will it show 12 volts and soon as the key is turned on? I put a new battery in today and the windows are working fine.

As I recall, power to the fuses comes straight from the distribution block. If you have no power to the fuses the problem will lie in the supply side wiring. Start at the battery and work forward to the fuse box.