In all honesty, while I haven't gotten quite to that part of the books, I've been kinda thinking about this a little bit too... Unfortunately, the magic gone over in the book really doesn't sit very well with how to do this period, much less at the speed your talking about Injun Joe transforming... I'd thought of a few ideas for a spell, or two that involve changing your form, but for the most part, they were only meant to be used as a form of quicker travel through more difficult terrains, not to be used in the sense your talking...
In all honesty, one of the bigger problems with trying to use a spell, is the fact that unless you build an additional "something" into the spell, in my mind, the transformation would be complete... IE Permanent. Duration doesn't matter at that point, once you've completely changed the body. In fact, what duration would do, would be how long the spell's energy could keep it going. If some hack job sorcerer transforms someone into a newt, and places a duration of a day and a night, the poor guy isn't gonna turn back after 36 hours. That'd be when the magic that is keeping his "not even a real newt body" alive, and without it, won't manage to stay alive for long... So in order for your spell to turn you into something and back, you'd most likely have to work in your SELF into the spell, a grounding point that reaffirmed yourself and who and what YOU are. Or maybe the spell, rather than changing your own body, simply creates a construct of the "form" you wish to take, hiding your own body somewhere, and pretty much placing your consciousness inside. You'd again, have to place some measures that allow you to get back, otherwise the previous version would be just as lethal...
I'm not even going to get into how I would probably do the spell, because I've found myself to be VERY monstorous on the required complexity of such things... >.< I actually tried to write it out, and I think I came up to a 62 complexity spell for turning into the equivalent of a Werewolf from the Template section, hehe...
But back onto Injun Joe... Like has been said, although he uses "magic" for his form of shapeshifting, taking refresh for his shapeshifting abilities and calling it being done by magic would most likely be the easiest way to stat it out. It would ALSO make good on the fact that hes simply ingrained it so deeply into his magical abilities, that he can cast such a complex spell at such a quickened rate. In all honesty, when I imagine how Joe probably started off, I can easily see him first making a spell and playing and mastering it. Over time, he began to get better and better at it, eventually getting to the point where he actually bought some Refresh stuffs. Now, I also imagine he probably started out with a single form. But as he grew older, and more powerful, he began working on others. At this point, I figure he and his ST worked something out, and he got to trade in his original Shapeshifting powers, and take something like Modular Abilities. From their, he could pretty much start taking any animal form he wanted. He also probably learned an Improved form, allowing him to shift to his new form even faster.
Of course, this is all speculation, and could be very very far from what happened... Its just what I saw, in my own imagined sequence of events.