1999 F250 Super Duty 4wd

This morning the truck would blow air, roll down windows, radio on, and turn on wipers without the key in the ignition. Put the key and the truck would start, pull the key and all those items would continue to work. Batteries Volts are 12.4. Tested while disconnected. There was some reports on this site of this being a GEM issue. Some were saying the windshield tends to leak and corrodes the connection. We pulled out Fuse box and GEM. Both were dry and all the connections were clean. We re-installed the fuse box and GEM and connected the batteries. Nothing electrical works now. I mean nothing.

We disconnected the batteries and pulled the fuse box and Gem again to make sure we didn't bend a metal tab over or miss something. Everything looked fine. We re-installed and no change. Nothing electrical works.

On the GEM box there is 3 places down the left hand side to plug in a wiring harness, but we only find two plugs and can only recall disconnecting 2 plugs originally.

Let me know what you think our next step should be and if GEM should have 3 plugs or just two.

Thanks,
Trent