A constructive failure
Unfortunately my project is not fully functional by the time of the presentation. I will consider this as a constructive failure and try to identify what went wrong this last week. Although I am (almost) sure that the device and the code are functional, there must be a bug somewhere messing with the whole thing. I suspect that this bug has to do with something specific to the XMEGA's, as my LCD/Wifi module was working happily on the atmega328p. I will try to debug this asap and update with the working prototype.
1. When a board doesn't mill correctly, mill another one and do not try to solder-fix the broken one. I spent 3 days only on iterations
of the electronics board because I was always patching bad designs instead of redoing.
2. Read CAREFULLY the datasheet of every compononent you use. I was using 5V to drive the xmega's only to realize a day later that the
operational voltage was between 1.7 and 2.6 Volts. I certainly could have saved some time here if I used the atmega328p, but I wanted
to push forward and get the advantages of the 2MSPS ADC.