Thanks for sharing this project - 3D printed custom case looks great. I noticed a couple of things like @ScruffR with your use of voltages. I would add 100nF capacitors in parallel to the resistors you have for the switches.
The Lipo battery you are using is 3.7V what is that connected to on the photon - the Vin, does this work OK? Also, the Lipo battery fuel gauge what advantage does this give over splitting the voltage output from the battery with resistors to ensure a range of 0-3.3v and putting this into one of the analogue pins?
Does the barcode reader not work with 3.3V TTL? My experience and since most of the digital pins on the photon are 5V tolerant is that as long as the peripheral is powered correctly the logic signals work fine. Surely you could take out a bit of complexity 