Diesel Bombers - Programming issues

Long story, will try to keep it short as possible. I bought a Smarty Jr. for my 2003 5.9 Cummins from Thoroughbred Diesel. Recieved it and when I first initially went to connect it to my truck I hit ECM Update....Connecting, Please wait...ERROR 20, Program aborted. I then removed it and tried again, same thing. I wasnt home at the time so I drove the truck home and that night, I went back out to the truck and tried again, same thing. I tried over and over to get it to connect. I got the same error everytime. The one time outta the blue after trying about 30 times, it connected to my truck. Showed SW: Stock of course, I hit continue. Asked which SW level do you want to program, I chose SW: 3. Programming 0%... ERROR COM TIMEOUT. NOW the truck will not start. Plug in the Smarty, it trys to recover back to stock becuase the previous update failed. I hit program to stock, Programming 0%.. EORROR COM TIMEOUT. Every single time. I tried more time than I can count. I emailed MADS/SMARTY they said that Error 20 is a communication error between the Smarty and my ECM. They recommended that I check and clean all grounds. Check and Clean the OBDII port. Remove the ABS/FUEL fuses. Check for low voltage on batteries. I did ALL of those things and it still did the same thing. I then called Bob Wagner and he had me unhook my positive battery cables to reset everything. I did this numerous times and still truck would not start. I called Bob back and he said that I had an ECM issue. That was it. So I ordered a refurb ECM programmed to my VIN, mileage etc. Installed in the truck, and it started right up and ran fine.

I was able to send the Smarty back and get a new motherboard put in it, since it was VIN locked. I received it back in the mail yesterday and went out to the truck with low hopes and sure enough, ERROR 20 PROGRAM ABORTED. I unhooked it and put it under my bed. I will not mess up a ne ECM like last time until I can figure this out.

I have done every single troubleshooting step that MADS and thoroughbred diesel has told me to do. They are all out of options. I contacted MADS this morning and their only suggestion is that I have a wiring issue and to check the wires between my OBDII port and ECM. There about about 1.4 million wires unders the dash that those 8-9 wires go into. There has to be an easier way to check these wires other than cutting my main wire harness loose and checking each wire.

Is there a diagram or anyone that can help me out checking these wires. Which pins on which plug does the oBDII port go to? Color codes. etc?

Any help now would be extremely appreciated. It makes me sick that I have a 500 dollar paper weight sitting here.

Thanks again