I agree with everybody else - DON'T BURN IT! Splash was dead on regarding the hanta virus. I woudld recommend you use bleach, as it is a disinfectant. In my younger years, I was a veterinary technician and we used bleach on EVERYTHING. It is a great, low cost sanitizing agent.
Dave's advice to take it to the car wash to use their canisters was a good one. There was also a post earlier this week about mouse mess in this same forum, and another bolter had a disinfectant/deoderizer he'd used on his truck. I'd recommend you take a look at that too.
Getting rid of the mouse nest and waste is no big deal, but you have to do it safely. You also want to get rid of the smell to prevent more mice from being attracted to your truck and ruining your work.
Good luck,