I got my replacement board from divemaster today. The good news is it worked on installation. The bad news is I'm even more convinced the problem is with the optos which are unchanged between the two boards.
I'm attaching pictures of the boards. The old board is on the left. The new board is on the right.
Although both boards carry the "Rev. D" identifier, they are clearly different board revisions. The only difference I could find (besides the screening) was that the crystal traces are now routed on the bottom of the board instead of the top.
As for parts, R1 was changed from 1200 ohms to 680 ohms which doubles the current into the diode side of the optointerrupters and could help in driving more light out of the diodes. The crystal package was changed as well and no longer bonds to the top of the board. The part number is changed from T06.000 to 6B0000B8AB.
The opto (ALPR0J0001-HC) and USB controller (HT82M98A) are unchanged between the two boards. This is disappointing because I still haven't found a source for replacement optos.
On the new board, the voltage drops across the phototransistors are 0.5V and 0.9V, compared to 2.5V and 3.5V on the bad board. The high voltages indicate that the phototransistors are not being driven 'on'.