Does the Y axis finally home properly???
You "may" have a problem with the setup depending on what bob you use. One of the pins on the parallel port is "inverted" (I think from memory it is pin 11). This caused me many headaches when I was setting up mine!
I also notice you have a thread on backlash and this also messed up my homing setup. I had to turen backlash off in order to get things working. (solved the problem by eliminating the backlash and used ball screws)
Art
AKA Country Bubba (Older Than Dirt)