For the sake of clarity, do I post the same instructions with a few substitutions? 

Well, um... no (for now).

Take the last log, start with this, and switch all the 4.9 kernel references for 4.4.91-ti-rt-r136 and here we are.

Well... that's not working either.

Traceback (most recent call last):
  File "arcus_3d_c1.py", line 23, in 
    hardware.init_hardware()
  File "/home/debian/Arcus-3D-C1-BeBoPr/bebopr.py", line 26, in init_hardware
    prucode=prubin, halname='hpg')
  File "hal/cython/machinekit/rtapi.pyx", line 219, in machinekit.rtapi.RTAPIcommand.loadrt (hal/cython/machinekit/rtapi.c:5233)
RuntimeError: rtapi_loadrt '('hal_pru_generic', 'pru=0', 'num_pwmgens=3', 'num_stepgens=4', 'halname=hpg', 'prucode=/usr/lib/linuxcnc/rt-preempt/pru_generic.bin')' failed: Operation not permitted
Shutting down and cleaning up Machinekit...

Now I'm confuzzled.  

Working on it..

EDIT: Figured it out with the help of Machinekoder.  

The wrong pru overlay was being loaded in /boot/uEnv.txt.  Commented the other one out, uncommented the following, rebooted, and it starts now.

###pru_uio (4.4.x-ti & mainline/bone kernel)
uboot_overlay_pru=/lib/firmware/AM335X-PRU-UIO-00A0.dtbo

 Estop loop is still screwy though.