That whole project is so nifty--very well done; Magus in CT is quite cool.
But back to the topic at hand. Nothing is explicitly stated, as far as Magus being Guile goes. He has no memory and he wants to fulfill a mission, I believe that's all we know. Could he be Guile? Certainly. Is he? Without definitive proof, how can we know? People think Magus is a whole load of people at this point: Guile, Serge, Wazuki, and any other random character. Sure I'd like for Guile to be Magus, but at this point I'm with Boo on this one: I too prefer to think we're being set up for some kind of weird Magus adventure, full of retcons and seemingly implausible material!