Thank you for the information. I removed the unnecessary parts in my code, as we currently were not using the OLED screen. Since we are not using the screen any longer, I2C is also no longer being used. All switches on the two boards that were not working as well as the boards in the field are where they need to be, so that is likely not the issue. I also was using the code snippet button, but it posts my code into this exactly like it did above in my original post.
I tested the twos boards that we had issues with again, and the one that we believe has a short is still acting like it did before, where my computer can tell it is there but cannot upload anything to it and it starts to heat up. The second one that we had a logging issue with appears to be working now, so that has been resolved.