Well I think whatever happend to the ESC also fried the RX. It seems the only channel that really works on the RX is my Throttle, none of the other channels will power a servo. I will probably end up picking up the Phoenix 35 and a new AR6000 and get the Align one replaced and send the fautly AR6000 off to Spectrum for repair. I can e-bay those to recover some of my costs once they are fixed.

It's still a little wierd, I'm unsure which part is faulty, although I'm nearly 100% sure the AR6000 is dead - or at least mostly dead. I also think the ESC won't give signals unless it sees the RX correctly, but maybe not.