How to help my malnourished rescue dog?

You need to be careful how much you feed him. Being skinny, means (since I'm sure they tested for medical conditions) means his stomach has shrank as well, from lack of food. If you feed him too much this can hurt his stomach and give him some serious GI issues. You need to feed him a rich, fruit and veggie (meat too) enriched foods, not store brands. Try going to petsmart and finding a good, healthy food for your dog where real meat is the first ingredient, with no corn or wheat-gluten. Brush him everyday and get him some doggy perfume- this can last (one spray) up to 5 days for smaller dogs. Hope he gets back to health soon.