1) it works exactly like you did. A cleric knows every spell of his level or lower, and prepares each time a total of his level+1 spell levels. The wizard knows 3 first level spells at the beginning and learns another spell of his level or lower every time he levels up. He prepares his spells just like a cleric (as many of spell levels as his level plus one).
2) you can perform animal moves with those holds, but until you spend them all, you can remain shapeshifted and do whatever you like. Also, you can just shapeshift again as soon as you have spent your holds. Class damage never increases with shapeshifting unless you take the "Red of Tooth and Claw" advanced move. However, when you turn into a bear with the "tear them apart" move, you really don't need class damage.
1a: it never happened in my games. I guess however you just change your alignment like you could do at the end of a session. That said, you should work as a group to find a solution that satisfies everyone, like always when doing something that's out of the book ;)
2a: uhm, my reply to this is the last comment in this post:
https://plus.google.com/u/0/107560837065764678288/posts/E5BFwFmJPqs3a: are you suggesting a custom class? The internets are full of custom classes!