Let me start with 
I'm watching this for sure! I've got a few remarks after looking at the schematics. I presume you've got the bm1366's connections from tracing the signals on a hash board and not from an 'official' repair guide? There are a few things that stand out to me and might be worth looking in to;
- the mode_0(in) and mode_1 signals are connected together.
  &&
- the decoupling caps c4 & c16 are connected to to these pins
  To me it seems as both pins are actually ground (vss). You can check for connection of these pins with the big ground pad to see if that is correct.

- the mode_0 pin is left floating for mode0
  Antminer has previously defined mode0 as mode_0 pin connected to ground.

Changing the description of these pins and of the mode does not change the functionality of anything but seems more correct to me (if the 2 connected pins are actually vss).
Did you find a way to log the communication with the hash boards or are you going the software disassembly route first?