What you're describing is 'function layers' ... layer 0, the default, they're Ctrl/Alt/Shift, but in layer 1, or some other lower layer, they're arrows.
I haven't yet seen a hinted at software for reprogramming the FaceW boards, but they're avr-something based, which is a known / fixed problem. I
think you could just use hasu/cubuniac's software but you might have to adjust the matrix. Actually I'm sure the wires aren't criss-crossing in exactly the same way as, say, the phantom. So once the exact matrix layout is known, it's a simple process to describe this key's meaning -- for each of the layers you describe.
One of the major reasons for choosing a custom PCB for a DIY kit, in fact. You can just reprogram the keys. Over, and over again. Whenever you'd like!
I plan on having dedicated arrows -- RCtrl can be in a lower layer
