I finally got around to getting the electronics up and running, but there are some discrepancies with datasheets and PCB errors holding me back. The PCB i received was missing the power-in trace to the boost converter, which I am having problems with as well. The datasheet for the SP6641A 3.3v boost converter says it can have an input of 1.5-4.5 volts and output 3.3v even. However, in practice it produces anywhere from 3.3 to 3.8v, enough to pop some parts on my board. To fix this, I plan to order the 5v version of this boost IC (drop-in replacement) and feed the output into the MIC5205 3.3v regulator. This should give me an even voltage across the 3.1-4.2v battery range. For V2 of the board, I want to make it smaller so less of it is under the propeller blades (maybe some smaller props are in order as well?) to increase efficiency and decrease weight. An all-in-one boost/buck IC will replace the two separate circuits as well.
To top it off, I the debugger can't connect to my PIC32 and I have no idea why. So is the life of an electronics engineer.