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One option might be to create complementary pins in your userspace module and link them in the HAL layer.

Can you give more details about what you are trying to do? There are a few examples of existing drivers with realtime and userspace pairs. These tend to communicate with private shared memory.

linuxcnc.org/docs/stable/html/man/man1/halsampler.1.html
linuxcnc.org/docs/stable/html/man/man9/sampler.9.html
For example.

Are there any updates on this? I am facing the same problem using Lcnc 2.9.4 and Gmoccapy 3.4.9. My touchscreen is recognized as eGalaxTouch. In Axis GUI and Gmoccapy with USB Mouse it works flawless. 

Does orienting the spindle motor work to orient the spindle? (If it's not an exact 1:1 drive ratio then it won't)

What does the motor orient to? Is there a programmable alignment offset?

You say you are running out of IO. Is this because you are using a parallel port?

I can't advise on your PCB design, but I think this looks like a nice idea.

I have occasionally thought that there should be a niche for a similar board, but with on-board stepper drivers (Trinamic or some other serially-controlled driver)
That would, of course, need a dedicated HAL driver, but those can be surprisingly straightforward.