I also like the "Master as Doctor" theory, and it would have made a much better introductory storyline than Twin Dilemma.
Hober, are you only going to watch the existing stories, or will you also seek out the soundtrack recordings for the missing episodes? There are several box sets available and last I looked they'd covered all the missing Hartnell stories. I don't know if Netflix does CDs though they may be available on iTunes if you're into that. Also, there should have been a 2-parter tacked on to the end of The Daleks, "The Edge of Destruction" which is a key episode because it set up a number of elements of the series some of which paid off in 2011. There should also have been a 30-minute condensed audio version of the missing story "Marco Polo" which if nothing else would help bridge the gap between Edge of Destruction and the next complete story, Keys of Marinus (which I warn you isn't particularly good, but the season gets better after that).