MorphVox is a good voice changer, too, and it's a little cheaper.

I've been acting for a long time, and I can tell you that if you're throat is hurting, you're probably working your larynx too hard, and not letting the rest of your breathing system do the work. Most of the effort for extended speaking needs to feel like it's coming from the bottom of your lungs, not the top.

Before you speak, you need to take a really deep breath, and evenly squeeze the air up through your larynx. If you have someone who can help you, have that person stand in front of you, and push his or her fists into your stomach (just far enough to make contact). When you breath in, you should feel a strong pressure increase against the other person's hands. If you don't, you're not breathing deeply enough. As you speak, the pressure should increase; if not, you're just lettting the air rush out willy-nilly, instead of in a controlled stream. By letting the air rush out so fast, you're making your larynx fight to keep control of the sound against the air, instead of letting your diaphragm do that work. This dries out the larynx, which makes it hurt, and it tires the larynx, which makes you hoarse.

Related to that, turn your head away from the microphone as you take your breaths, so the mic doesn't pick up so much of the air sound. Also, before your first speech, stretch your mouth out... try to stratch your lips down, up, left, and right, stick your tongue out, that sort of thing. It looks silly, but it helps your performance a lot.

As for your characters, I would agree with the idea of doing all your lines for one character first, then do the next character, then edit the lines together. A lot of professional animation is still done this way, to accomodate actor's differing schedules.

Another thing you can do is to improvise with your characters. Try it on your family and friends (if they'll put up with it, of course; I get varying degrees of support from my friends...); just have everyday conversation using your character's voice and mannerisms. I do improvisation exercises with a drama group I belong to, and it really helps your acting in general. It will also help your writing, too; you'll have a much better feel for how your character thinks by acting in real-world situations.

Hope that helps.