Cummins ISX problems

The truck is an 04 International 9400i, with an ISX. Last week while going down the road the truck suddenly shut off, and would not refire. It would turn over, but with the key off and out of the ignition the blower motor and low air pressure warning tone were active. I looked in the battery box and the two fuses to power the ECM were blown. I replaced them, went to start the truck. Turned the ignition switch on and it went through its cycle and then everything turned off. I tried to jumper around the ignition switch and nothing happened. I reseated the fuses in the battery box and the truck started. I then tried to plug in the ignition switch again and nothing would power up. I have replaced the ignition switch but with the same results. Several times when I put the jumpers on it will either be dead (no power to anything) or can hear the lift pump but wont crank. I reseat the fuses in the battery box try again and will start with the jumpers, but will not with the ignition switch. Does anyone have any guidance as to where to start with this?

 

I have traced all battery cables including alternator. Replaced a ground from starter to engine block.

 

What I cant understand is why the truck will start with jumpers plugged directly into the connector for the ignition switch, but when I plug the ignition switch in there is no power to anything.