Mysterious pulses on input pins

[Demon]

...Turns out I had dead LCDOUTs at the very bottom that were sending pulses to default pins...

Ioannis, you misunderstood. Dead LCDOUTs, not dead LCDs.

I forgot to take out the commands when I migrated from my breadboard for preliminary tests (on the left), to the larger circuit on the right.

Now the rotary encoders and ADC are handled by the PIC upper left, switches will be handled by upper right (not implemented yet), USB will be lower right and outputs are handled by the lower left (LCDs and future LEDs).

The right side is not implemented yet. I wanted to get the 16F18877 on the left working properly first (IOC, ADC, PWM, USART, that sort of stuff).