does anyone know why my brake pedal fades away to the floor after putting 1 ton running gear and 4 wheel discs with the e-350 master if so please help!

The only two things I can think, assuming you don't have any leaks, is a bad MC, or air in the line. Are the callipers all in good condition?

its all new stuff including the calipers it only fades away when the truck is running

This may give you some insight.

http://home.4x4wire.com/erik/4runner/brakes/