I had a similar problem where a squirrel tore up most of the hood insulation and stuffed it in every nook under the hood, and a friend of mine who works at a tractor supply told me what they use to keep rodents from nesting in their cabs. They're basically satchels full of a strong-smelling cloves and some other stuff, totally organic and not unpleasant-smelling. I hung one from some wire under the hood of each vehicle and the little bastard hasn't returned so far. The satchels aren't exactly dirt cheap, but they last several months and it beats the hell out of having to repair the damage those critters can do.

Ask at your local farm supply and they'll probably have something similar.

Amazon has an organic mint based rodent deterrent that just smells like thin mints. Got rid of a squirrel from my attic not too long ago.