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I am trying to figure out how to make a unit hover like the Emperor does(when he is idle, not when he is flying). Is it a skeleton thing, a combo script, or something else?

To be honest, I think it has to be his basepose in the animations. I could be wrong.

I don't think it could be that, unless it actually is the model touching the ground.

It's just his idle animation, and yes, his model "touches the ground" (appearance is really irrelevant).

So, I would need to add something to a model, and add the idle animtion to the unit that I wanted to hover?

You just need to use the animation. The Emperor's model is the same (effectively) as anyone else's (as are all the humanoid models in SWBF2).

Thanks, I will go try it out...

And can Blender+MSHViewer modify existing player models(I think not, but want to be sure)?

No, they cannot.