Excellent progress this weekend on the laser tag guns. The latest board featuring the ATSAM3X8C along with a handful of QFN packages was the first major success. This weekend I found a number of said chips needed re-soldering as I cautiously handled power management issues and made changes for the newest board revision. Yesterday I got the 3V3 voltage regulator working along with the LiFePO4 battery charger. The charger runs a heft current and is going to need a larger thermal plane to dissipate heat.
The next major accomplishment was getting the USB device recognized by my computer. I followed this article to install the right drivers. You can use either BOSSA or SAM-BA app mentioned. I was able to follow a workflow pieced together from many forums and videos to finally get the (non-evaluation-kit) SAM3X programmed via USB. The below screen shows the confirmation that the flash was programmed. Unfortunately due to board design mistakes I need to order new board before I can do much more from this point.