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Although the lines are apparent, there was still no communication from minicom 😞 . This leads me to believe that it might be a FW issue rather than signal integrity, as both these MCPs failed to communicate. Investigation to be continued.
Another day in the solar sense troubleshooting, and I just figured out how to decode I2C on the scope I was using. I set everything up only to see the 3V3 line go high then slowly decrease to GND potential. After a while (~1hr) it was clearly shorted to GND. I then spent the next ~2hrs trying to find the short, and then eventually removing every component on the 3V3 rail with subsequent checks if that fixed the short. It did not.
I then removed the solder from every pad on any component interfacing with 3V3. There was still a short until I removed the solder from the pads of U2 and C6. I then did not see a short (and ofc this was these were the last pads which solder I removed). Turns out there was a short to GND on pad 1 of C6 to the GND plane. This was due to the clearance from polypours which as can see from the image below, is not very large. That coupled with manufacturing causes a short with solder on the pad, and so i cut the right side of that pad. After this point, it is fully isolated. This was a very unfortunate issue (as I still have to put all the components back on including CB connector) but at least I now know for rev 2 that I should put more clearance.
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