Chris,
Your transformer is a Shumacher. Look at the schematic that Loudthud sent. This is for a 2000S amp, but has the same power transformer as the 1000S. If I understand you correctly, the wires you mentioned are still attached to the transformer; namely, the blue, blue/white, blue/black and black are all primary wires. The green/yellow wire is the center-tap ground on the filaments (secondary). All of these match the 2000S schematic. It appears (from the photos) that the rest of the secondary wires are still connected. You should find the following: two yellow wires connected to pins 2 & 8 of the two rectifier tube sockets (5AR4/GZ34); two red wires connected to pins 4 & 6 of the rectifier tube sockets; a red/blue wire connected to a terminal strip (this is the negative bias feed); a red/yellow wire connected to ground (the chassis); and two green wires connected to another terminal strip (these are the filament wires). Take your amp to a local tube amp tech! High voltages are involved (read: can kill you) so you need someone familiar with vacuum tube technology. This should be an easy fix.
Good Luck!
Ryan