Problem geting basic config running

Thanks John, turns out I was not driving the LED's hard enough. My spindle encoder is now happy.
Any Idea What the joint on limit switch could be? I have the inputs present, and I can pulse them manually.

I have answered my own question - Limit switches were inverted polarity. I run my switches and spindle encoders active low, should I invert the encoders as well? The RPM does show action if I pulse the phase inputs, no idea if it accepts my index, but scope shows it as active.