Hey guys, just wanted to say we got it figured out today. Storm Ninja prototypes program just fine with energia and the pins I tested so far seem to work.
Here are my notes for getting a bare Energia 13 installation working with Storm Ninja (and with the 5969 for that matter which doesn't work without a dll update)
boards.txt contains high level processor speed protocol etc. under hardware/msp430
an entry duplicateing the lpmsp430fr5969 entry is required to add a new variant.
then the prefix should be changed from lpmsp430fr5969 to stormninja
additionally the line xxx.build.variant s