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Yup still there.
today's download  and install yields this report on terminal
 

after running sudo dpkg -P raspi-firmware
terminal yields this report
 

Sorry tommylight I know it's always something. I will just put a note with
my install disk ( yes I still make disks instead of thumb drives ) LOL

thank you for the quick response!
I am not sure what you mean by beginning of the next cycle.
If I remember right, the samling of rows is done with 3.7kHz scan frequency and each row is measured for ~30µs.
From my understanding the inputs should be sampled at the end of each cycle so here ~25µs after the output is set to low. So right before it is set back to hi-z.

I have a dual-Y configuration on my cnc, and what I have is two limit switches - one for each motor. The config has a separate section for each *motor* so you can specify the homing offsets independently. In my case, the two entries differ by 0.036 to bring the gantry into square. So I'm using your #3 solution I figured out the offset value by homing, measuring how off-square I was, updating the config, and re-homing; repeating until it came out square.

Your alternative is to mechanically tie the two motors together (or use one motor and two screws) and tell linuxcnc you only have one "motor"

Looks like the drives were originally setup  for up/down
(Pulse F, Pulse R in the drawing) mode so you might try
setting the 7I96 stepgens into that mode. 

(step_type = 1)

Why are you using the stepgen board?