Whole lot of "nope" today

 CARELESS LOW COST MANUFACTURER LABELED USBMOD SIGNAL WRONG

I got the data sheet for the FTDI chip on the module in question, then verified that the WR signal from the chip is directly connected to the module pin that is falsely labeled #WR. It is not inverted. No problem.

COMMUNICATING WITH MY INTERFACE IN THE M1000, READER IS STILL BAD

I was able to connect over serial to my board and see it present status. To do this, I swapped in my good error board from the M600 and then watched as the external signals assumed correct values corresponding to changes in the reader state. 

DEBUGGING THE EXTERNAL INTERFACE SIGNALS

I see oddball and incorrect voltages on the output lines from my newly replaced 7417 chip to the external connector lines. I pulled the board and decided to continuity test all the traces to and from that chip. It was at that point, as I tried to verify the 5.6K pullup resistors on each open collector chip output line, that I found they were missing! No pullups which is a bad thing on an open collector gate unless there is an external pullup. The interface design I am using depends on the reader to do the pullup. 

Known good board has four 5.6K pullup resistors

M1000 error board with no pullup resistors

As I looked closer at that board, I see it is quite a bit different from the board in my working M600 model. For one thing, it has five additional ICs that don't exist on my working board. These are a 555 timer, a 7400 quad NAND, a 7474 dual flipflop and a 7404 hex inverter. 

Only the upper left chip exists on standard board

There are also two jumpers added to the board. One connects marked pads L and N on the board, which don't show up on the schematics I have. It is barely visible as a thin pink wire in the upper left of the picture above. The other jumper is a mod that must be implemented to change the board to work with the very slow models M200, M300 or M500, although it seems to have been uninstalled. In other words, the mod cuts the trace between C and D, then a jumper is put between C and E. This restores connectivity of C and D. 

trace cut C to D but 

Not sure why it had a modification and then was backed off. On the other hand I see jumpers and rework on other boards so it might have had boards converted for the 1000, pulled from other machines, to serve as replacements when prior boards failed.