Interesting, that was going to be my initial test to try and fix the display issue we were having in the first place; doing exactly what you did here and changing the busy pin in the inky code and wiring up a jumper. I think I’ll just live with the power button not being able to turn it off as my header stack is already a bit taller than I would like with 1 stacking header. Here is how I am setup now, I hope to still be able to mount this to a wall with some frame standoffs I will try and 3d print
This random behavior could be due to unclean edges, which are caused by the setup. If you have an oscilloscope, you could try to measure the clk-pin and see if it has sharp changes between 0 and 1.
And you could reread the Stack Exchange post I linked to above and maybe try changing the drive strength. That post is fairly old and I am not sure if this still works as advertised though. The author “Milliways” is btw. highly respected and so this sounds reasonable.
I wanted to update where I’m at after a few days of successfully running the Witty Pi L3V7 with Zero 2w and Inky display. I’ve been using it to power on my display and run a weather app every hour without any issues or the unreliably you pointed out. I also figured out how to fix the issue I was having with not being able to turn off the pi with the Witty Pi power button. After messing around with trying to clear/reset hung GPIO pins in Witty Pis beforeShutdown.sh script, I found the fix was simply updating the “Power cut delay after shutdown” setting in the Witty Pi settings. I changed it to the max 25 seconds and have been able to successfully use the button ever since to shutdown and reliably cut power. Seems like the inky software needs some extra time to settle down and let the pi power down fully before freeing up the GPIO 14 TXD pin, which is actually what Witty Pi uses to monitor the pi’s power state before cutting battery power according to the manual.
As for the unreliability you are getting with screen refreshes after the SPI fix, I wonder if that has something to do with the larger 13” screen you are using vs my 7”
It is really a pity that Witti Pi does not use the gpio-poweroff overlay. This is an elegant way to signal shutdown to external peripherals.
I don’t think the Inky software uses 14/TXD at all. It is just the shutdown that takes time.
Another trick I was using together with my Inky-Impression: I configured the system as read-only. You can do that using raspi-config in the performance section. With a read-only system, you can just cut power, there is no need for a clean shutdown. This of course only works if you don’t need to keep state. One solution is to add a small partition to the SD and only mount-write-umount when saving state.

