99 Dodge Ram 3500 SLT 2WD 5 SPD.

Engine wire harness was all rigged up with wire nuts so I replaced everything coming out of the PDC connector including the two firewall disconnects, everything going to engine, ecm, pcu with a harness from a base model 99 ram 2500 diesel 2wd auto. ECM fuse blows immediately, abs module won't turn off, I'm working on it now. Have grid heater system off, pcu disconnected... Still have short. Disconnected grey connectors near aux battery coming off negative terminal and going to large black and orange wire and the ecm 2 fuse loses it's short. Plugged that back in and disconnected ecm and short goes away again.

Also is there any difference from an early 99 to a late 99

 

Can't help you with troubleshooting, but the parts manual does not list an early harness and a late one, there are different harnesses for things like DRL, Fog lights, etc, but I doubt any of that would cause what you have.

 

Pin outs may be different manual to auto harness. This is where a wiring diagram becomes important. They shouldn't be different, but in the automotive world it is entirely possible. It sounds like your ecm harness has a power pin shorting to a ground point. This would be possible if there is a difference in how the ecm and pcm work together. And, auto to manual, there will be differences, for electronic transmission control.

Can you measure the current that induces the blown fuse? That would help a lot in figuring out whether it's a sensor short, or a bare wire to ground issue.

If the frame is energized, what voltage is it, 5 or 12.xx? If it is 12.xx, then you have something wrong in the primary circuit , starter/battery/alternator/charge.