Here is my 2 cents on that....
(1) There are lots of other posts by riders far more experienced than I who, I believe, did the route you are talking about. Try any of Gaspipe's threads on the Canyon. The guy is amazing.
(2) I admire your intent to do it solo - I would have too, but I enjoy the mob scene and have made many long time friends that way.
(3) There were zero what I would call challenging water crossings from Creel to Batopilas and back, to speak of. That, of course, would change during days of heavy rains. Watch the weather. I've seen photos on advrider of the same sections I crossed dry that had a bit of wave action going, but again, it's to be expected after a long wet downpour, as any rinding in canyon country is apt to provide.
(4) Water crossing aren't the only place you might, or will, drop you bike. That shouldn't deter you in the least, as there is enought traffic that will stop and help you pick up your ride.
(5) Going it alone is something I would do now that I've been through the guts of Mexico twice. I fell in love with the people, the language, and the orderlyness of things down there. In fact, in many ways I'd rather ride there than in the U.S.
Batopilas is WELL worth the effort to go find and explore!