Sorted the estop issues.  It starts up, powers up, and estop does what it's supposed to.

Either I wired the entire machine wrong, or now the PRU isn't generating step or PWM signals on my pins.

Everything in software now suggests it should be working..

My CRT oscilloscope is dead and given it was never that good to begin with and from the 1970's, I'm not fixing it.

So begins the task of looking for high frequency transitions on pins with no scope.

EDIT: I clipped off an 1/8th in headphone wire, probed the pins, and recorded the audio via Audacity for a ghetto scope.

Nope.  No PRU step or PWM output.