ISX 15 no power to ECM

I have a 389 2014 Pete dump truck with an ISX 15 - CM2350, it got into some pretty high water during this recent flood (was up to the bottom of the breather on the driver side) - I went to trying to fix it last Thursday - draining fuel, transmission, rear ends and flushing them, got to where I was ready to warm the fluid up for another flush and truck wouldn't crank, changed the starter and checked some fuses but turned out it was the batteries (should have checked there first).

Got truck running, ran good drove it around 30 mins (had a check engine light come on while driving it for VGT think it was 641 - but has thrown that code before and would usually go away) and came back, drained the fluids again and re-filled them and went to start truck and it would crank but not start. I started checking fuses again, found a small in-line fuse box in the battery box that had water in it but fuses where not blown so I cleaned and dried it out and changed the fuses just in-case, checked battery connections, checked all the fuses again (changed the 100amp fuse in the box near the firewall since it showed a little rust), checked resistance on VGT plug and it showed 135-137 ohms (from what I could find it should read 120 so i'm not sure if that is an issue or not) and checked harness plug with a light probe and it got power there but the light was weak, I then looked up the wiring diagram on quickserve and found the pins that power my ECM and checked both of the ECM connectors and could not get any power there with the key on. (also checked the grounds, removed the ones at the engine block and cleaned them up since I seen some corrosion on them)

All the marker/headlight/cab lights work, but when I turn the ignition on it doesn't show hours or mileage just the ------- lines. Has no codes on the radio diagnostic, but shows J1939 code on the dash. I read about checking the terminating resistors and that's partly why I checked VGT, but I haven't been able to find the other one, talked to a mechanic and he said it should be somewhere near the ECM/intake. I'm going to try to find it today and also try to run the small wire from the battery down and find out where I'm losing power. I'm not very good with electrical problems so I called a shop and looks like earliest they could get to it is next week. Any help or tips anyone could give me would be greatly appreciated, Thanks.

- update - I think I found the terminator resistor on the ecm side (was a 3 pronged connector that didn't go anywhere, measured resistance on it and got 120 ohms) - Thinking it's in the ignition switch or the small wire that runs from the battery to the starter

- update 2 - Changed ignition switch but still no change, Checked little wire from battery to harness that runs near the starter and it is getting power up to the harness junction (tested with probe) - decided to test ecm connectors again and I'm actually getting power on the J2 connector (bottom connector), must have tried wrong pins earlier, still no power on the J1 connector though (tried all of the pins to be sure), also took wires off starter and made sure they weren't broken there

 

- Took ECM out today and to a guy who could bench test it. He couldn't get it to pull up anything on the ECM so thinking some water got in the harness and made its way to the pins and shorted it out. Got a new ECM and should be up and running sometime tomorrow unless something else shows up.

 

New ECM and still same problem

 

Only big fuse I found in battery box is the 100amp but it tests good at 0ohm resistance there are also 2 other fuses in the little square box. Did find round connections took em apart and seem to just be a way to connect cables. black tape wrapped up is to a relay to the tarp motor

- just figured out how to check the voltage on fuse in cab beside the pedals (voltmeter one side to battery ground, other to fuse) and I was reading 13v at the ECM fuse, not sure if thats good or bad though, thought it should be 12v