For (1), there already exist databases like that. The most comprehensive one I've found is this one. It's not totally complete, but it still has many, many spells of all kinds. I counted around 6,000, though some are probably duplicates. It also has an extensive search function and some themed lists. I also counted around 3,000 cleric spells. I had expected the ratio to be higher, to be honest. If wizards only have twice as many spells as clerics, maybe it's not so unreasonable after all; at least in the sense that a player would be just as overwhelmed as if they had played a cleric.

(2) is an interesting idea. The main issue I have with it is that it will end up being DM fiat. I mean, if the PCs just finished up one adventure and are heading out on another completely different one, I can't arbitrarily deny them the ability to change their spells because a game session has already started. So I'll have to say, "okay, okay, you can change spells now." And there are other, similar circumstances where I'll have to override the rules. Also, I don't know how that could be justified in-game.

(3) is a very cool idea. I'm sort of aiming for him to be a good utility caster. Do you think that using schemas in this way would make it difficult for him to both contribute during combat, and still have the right utility spells for the job? How many spells/schemas should he have?

About the knowledge skills, you're right. I've pruned them a bit. For now, I have only Espionage and Warfare left, and I'm not sure where to put them. I can't with a straight face give him an ability that lets him make a Knowledge (history) check instead of a weapon attack :P I was thinking of claiming these skills are only useful for universal scholars, or that characters can make a Knowledge (warfare) check using their BAB instead of skill ranks, since it represents knowledge of combat.

I'm sort of working on a small overhaul of the class. I've changed the names of most things, and made them seem less silly and more interesting or fantastic. I've decided on dumping MP altogether and have him use his abilities by expending spell slots of similar level to the ability's power. For example, Theory and Practice costs an 0th level spell slot to use (or higher). I think this will make balancing everything far easier. I've tried posting my work, but I ran into the character limit (which I sort of forgot about...). I'll probably have to make a new thread with extra posts for more material, and I'd like to get more work done before that. I haven't changed the spell casting yet, though.