The board you picture is the I/O work like mine and there is a similar board attached to the display (minus the USB ports and some variation in population of the PCB).
From what I've been reading there are various revisions of both the I/O and the LED control board. and compatibility changes with both of them.
From what I understand the game pre-loads animations into the I/O board so that during gameplay it can just send simple commands such as "play animation #5". This makes sense because the JVS bandwidth is pretty slow and you'd have really laggy gameplay if the game board was providing the whole bit-stream for the display while polling the controls.
It looks like the communication between the LED control board and the I/O board is a simple Serial connection. Ideally I'd like to figure out if it's a 1 way output or if there is some kind of hand-shake communication that reports the LED control board revision/capabilities back to the I/O board and if it uses a standard/existing protocol for communication. ideally we could use an off-the shelf LED display/control board or worst case build one.
it could also open the possibility to improve compatibility across games that support it by reporting whatever hardware revision it wants to see.
If the I/O board does indeed store animations I'd suspect that it would be much more difficult to emulate, the JVS protocol is pretty well documented but I'd guess that these commands all reside in the "manufacturer specific" code range. so it'd be matter of recording the serial data and trying to make sense of it.