When cleaning cars, I first remove the shell from the chassis. I'll wash the shell in a very mild warm soapy water mix and go over everything with a soft toothbrush. Then rinse under clean water. I then pat it dry with a microfiber towel.
For the chassis, break it down as much as you can. Soak it in "Evaporust" until it takes the rust off. I've heard vinegar also does the job. It's probably cheaper and less toxic. Sand it thoroughly and then paint the components to prevent rust from returning. POR (Paint Over Rust) is a great choice. Be sure to lube all the axles where they go into the trucks, and lube the couplers and rollers, too.
When the shell is off is the perfect time to weigh the car and add weights inside so that it's specs meet what the NMRA recommends. That's how I've done my rolling stock, but I'm sure there are better ways I haven't considered. Good luck with your project.
Tom