So I rigged a Toon Link player model, but I'd like to downscale the ingame model so he is not so giant in comparison to the zombies and the environment. How would I do this?

maya has a scale tool, im guessing select everything then scale it down using that tool

Ive resized my batman models before and I just resized it in Maya like Harry said. If it's rigged just select the first joint, usually tag origin or something and resize it, that should do it.  Iv even made player models the monkeys from Acension lol and they are tiny. It's easy to do. 

The only way I know how to fix that is by moving the skeleton closer towards Link's stomach. But if you do that you will have to unbind the skeleton and re-rig him. I'm not sure if you want to do that but I believe that would fix your problem.

You could try to increase the distance from tag_origin to j_mainroot in the same way you do as with fixing ai anims from bo/bo2. But you would need to edit the prone animation then. Good thing about that is it will only affect the height in prone, and when you change the rig you prob end up with height problems for other anims.