I am truly sorry for the lack of detail in my question (it was written in a bit of frustration... )
This is a friends SideWinder X1 (stock config), a Raspberry Pi 3b mounted to the right side of the printer and connected via USB. This has been up and running with little issue until i added the Filament Sensor.
I have a similar setup of my own that I have added the same runout switch config (I have made an extension "Y" connector and pulled out only the signal and ground wires from the Sidewinders switch, to be connected to the Pi. This config is working on my machine and I tested the extension on mine before connecting it to his.
While connecting the extension to the Pi, I think i missed the correct pins (I am using a dupont connector so nothing gest shorted to the neighboring pins). When i connected the wire to his pi, i think i must have missed the correct pins because as soon as i connected it, the display on the sidewinder went blank. I immediately disconnected it and the display came back. I shut it down and powered it back up.
From the printer panel, I can home everything and heat the bed / hot end. I have not tried to print from the included Thumb drive yet because i didn't have it handy.
I logged back into OctoPi and tried to start a print job that i have printed earlier in the day. The Pi indicated that the print was starting, but the temp indicators never seemed to indicate they were turned on, looking at the printer control panel for this same job, there was no indication that the bed or the hot end were heating.
I took his Pi home, put my sd card in and brought up my installation and started a print without issue.
What I am afraid may have happened is the communication between the Pi and the printer may have been damaged in some way, i just dont understand what may have happened here.
There are 2 possibilities for incorrect connection that may have happened, #1 i connected between gnd and gpio25, or #2 I connected between gpio23 and gpio24.
Could this in any way have damaged the printers main board?