Sorry for the delay, summer vacation…
My guess is that there is zero difference in the schematics electronic components and signal names between most of the the Shapeoko controller boards except that connectors (and pinout) are of a slightly different type. It’s because the firmware is based on an open source project. Newer connectors are probably cheaper and more assembly friendly from cable point of view.
The PWM output goes directly to the mega328 uP and is unprotected. Be extremely careful if using the X12 connector as the unregulated 24V will potentially kill things… This is probably why you wouldn’t get any answers from support… no warranty policy for experimentation…
I posted some details about what can go wrong here: Feed Hold Switch - #69 by Norway
Signals between in the two connector are connect by name (wired on PCB). PWM is normally alternating 0V and 5V if using a BitRunner. The PWM duty cycle is else set by the commands as stated by @Julien in the “spindle ON” state.
I don´t have a SuperPID2 and it’s a bit hard to verify, but it looks correct based on what I’ve seen here: ShapeOko 2: SuperPID Upgrade! - YouTube. A bit confusing in this video @6:17 as it says that the PWM goes to the PC. It shall be output from the PC and input to the SuperPID2. Then there is probably a RC (serial resistor to a capacitor to ground) low pass filter where the average analog signal “equivalent” to you pot. goes from junction resistor-capacitor and output on terminal VS.
Wires connected to the 3.0 board should be PWM and GND only. This is my best guess. Good luck!