EWS and Battery charging issues

[B&K-X5]

Hey guys, I sure hope one of you can help me figure this out. I changed out my N62 in my 05 X5 after it was ran out of oil. I replaced every seal and gasket you can think of on the replacement motor including valve stem seals, and water pipe. I have spend gobs of money and time on this motor swap. After I finally got it running; I discovered torque converter got bent in change out process so then changed out tranny and transfer as long as we were taking it all apart again and was getting tranny and transfer errors. Finally get it all back together again and running and ran battery dead while scanning errors. Determined battery was bad anyway. Installed new battery and got it running again. Fox 530 told me I still had tranny and transfer errors also steering sensor error . While I had Fox connected I did battery register (I now know you don't have to register on E53) but too late damage already done. After that car is dead in the water and won't start. Fox told me EWS DME out of alignment. But Fox can't fix it. So I bought a cable and downloaded INPA but it terminated connection and couldn't fix it. Next I bought another cable and new INPA and DIS package with 5 cd's . We loaded that all in lap top and it is having connection problems as well. I determined it might be because voltage is below 12 volts. Even with battery charger on it. So what I started realizing is battery charger is getting hot and one of my chargers at 13 amp even kicked out trying to keep battery above 12 volts while trying to use DIS. It is as if the car senses that it is being charged and doesn't let the charge go to the battery; it instead just shorts it out or something. With battery disconnected from car it is taking a charge. I obviously have to figure this problem out before I can get the EWS aligned. Anybody know what this could be ?