Excellent work here! very clean design  :)
would you be open to sharing the DC-DC circuit posted above?  Doesn't appear to be in the eagle files listed - thanks! :)

Why don't you use the charging interface of SIM808?

@Francesco  i do not know why i do not find your comment earlier...:-(
1.) as the reset problem... indeed i have never find this problem before... and do not know if this is  design, or production problem. compares to Arduino official zero design, the only differnce i can see is Arduino zero added a 330 ohm resistor serial connected.. i do not know if that is solution to solve this  problem, i will need to have a try to find out the problem you mentioned in my boards firstly;

2.) as the SD socket, i select this hinge just because there no engout space for a  push-pull type.  need to check if the vendor quality not good enough.  and the pin breakout, really a problme, need to consider to breakout the SPI pins
3.  the Bluetooth now availible , with added bluetooth antenna, in the latest version V3.5.. as the audio input/output,  i considered this module is mainly for IOT application and audio not used.  i have to disgard these pins when there is not enough space

I bought a Maduino Zero v2.0 about a year ago and, overcoming many difficulties (mainly due to lack of documentation and support), finally I managed to build a complete GPS Tracker/Logger with many custom features.
I think that the Maduino Zero, altough a good idea, should be thorougly revised to improve first of all the reset circuitry; I say this because, when I reset the board using the pushbutton, in almost all cases the SAMD21 doesn't restart correctly; indeed it shows a random behaviour and in the majority of cases I am forced to repeat the reset many times until it restarts correctly. Also the software reset at the end of programming doesn't work correctly.

Other problems I see also in the current revision of this board (3.4) looking at its schematic diagram and layout are:

- the poor quality of the uSD-Card socket that in my case was broken just after few days of normal use. I think that the "hinge" type of socket is not adequate and a push-pull type should be better;

- the main SPI signals (MISO, MOSI, CLK) are "reserved" for the uSD-Card and not available on the I/O connectors; this is a serious problem in case one wants to connect other SPI peripherals to the board (like a display in my case).

- the bluetooth and the audio IN/OUT functionalities of the SIM808 are not available at all; they should be as in the majority of SIM808-based arduino shields

Glad to know it works OK now. Thanks for your updates about the usage

Anyone use this device, I am having issues with it that I cannot figure out. I cannot detect the serial port.

https://stackoverflow.com/questions/50360616/why-is-makerfab-sim808-atmega328-serial-port-not-showing-up-on-arduino-ide-on-my