1) Verify components are working individually using a PCE-1 or PCE-2. Shifters, derailleurs, and Junction A. The small diagnostic function of the charger only works if the system has integrity (which you don't know yet).

2) After verifying that the parts work (or do not), replace any [suspected] damaged E-tube wires with a known good one.

3) Once the system is properly connected, and you know you have no broken components, do a firmware recovery using the PCE-1/2. You should then be able to update as normal.

Note that putting incompatible parts in the system will also cause it not to function properly (mixed mountain/road derailleurs, d-fly with 1st gen batteries, etc...).