The Mark V90 method of channel change logic would not be suitable for running parallel to two amps. Not only would you be coupling the power supplies to each other by some common link, it probably would not work. The Mark V90 uses a voltage level to address channel switching when using the DIN cable. Also, making some sort of parallel cable to connect to both amps could result in current sourcing between amps if the 24V, 12V and 5V supplies are slightly off from each other. That may damage some internal components. If you think that would work, consult Mesa customer service through email first as they know their product well to provide technical information to guide you in the right direction.
You have two options. Each would require some sort of midi control unit.
1: use the 1/4 jacks on the back for channel change. That would only give you the 3 channels, EQ and Solo. It will not be able to control the FX loop. You would need to find a minimum of a midi controlled dual relay module for channel change or if it has SPDT relays, it may be possible to make use of just one if the relays are isolated from each other.
2: Mesa Boogie Midi Matrix. Supposed to be compatible with all Mesa amps. You would need two of those as well, one for each amp.