OK - I rerouted the board, it's laid out better now. All components are on top, traces are a bit less of a mess, I added a few 5v/ground headers on each board, and I connected S1/S0 properly so the boards will (or should at least) work in a single chain.
Can someone please confirm it is ok for me to bridge (1) pin 7 to pin 8; and (2) pin 9 to pin 10 (the serial and latch clocks) on the J1/J2 headers? Looking at the MBHP_DIO_Matrix schematic, it looks like this should be ok.