First off, using individual jumpers sucks.  This choice alone has probably cost me 20 hours of debugging time.  Some pin header ceases to fit perfectly and you partially lose ground, which makes things fail only when the majority of signals are above the halfway point between ground and Vcc as the the low going pulses also provide a partial ground.  Argh.

Narrowing this down to the jumpers happened when everything finally got hand soldered directly, and all the strange issues happening during testing just went away.  

Hand soldering wires still also sucks though.  So I have now specified pre-made IDC connectors and matching keyed sockets for all the internal connections.  

I have also settled on using an RJ45 connection to our current #VISP - Ventilator Inline Sensor Package module which uses dual I2C, by splitting the four pairs of wires of the Cat 5.  

One leg of the each of the four twisted pairs will run SDA1,SDC1,SDA2,SDC2 and the other half of those four pairs will run our Vcc/ground.  This seems to be a reliable way to get what we need for running dual I2C channels, out of an existing and robust connection like RJ45.  Much more so than trying to run the SDA/SCA on a single twisted pair anyway, as they essentially work against each other then as they are not intended to be halfsies of a differential signal.  :)  

This also probably means generating two tiny daughterboards just to make our IDC to RJ45 jack connection, and to plug into our new optical interrupters, but so be it. Reliability is kinda key here.  Which leads me into the next design choice.

Using unshielded hall effect sensors anywhere near a DC or stepper motor, unless they were designed for that particular motor, also sucks.

They will read perfectly, until you start your motor (if you are lucky).  If you are not lucky, they may still read perfectly.. for a while.  Eventually though it seems they reach some saturation or auto-leveling point, and cease to work reliably until you remove the field generated by the motor/stepper.

Our hall effect sensor for detecting 'home' got replaced by optical gates and a laser cut encoder.  I also attempted to future proof this bit by adding a second encoder we could use to read the rotational rate.  That led to four more design variations on how to space the encoders/encoder slots.  I have arrived at the final revision for this.

I've built out a single glue board for hooking all of this up.  Assembly and testing will happen tonight, if I don't run out of steam.