Sorry it has taken me so long to get back with you!!
Mayfly is right about the towel. It is easy to keep from getting scratched if you wrap three legs tightly with a towel while you clip the fourth paws nails.
Some cats are just have really bad aim when it comes to coverng up their messes. My cat is like that. She will go, then turn around to cover the mess but she misses every time. The hooded litter boxes do help in controling odors. If you want to go a step farther, you could get an automatic litter box (called the Litter Maid). Each time you cat goes, it will automatically scoop out the clumps and put them in a plastic box. Once the box gets full, you can either throw it away or clean it out and reuse it. You can get them at pet supply stores and I have seen them a few times at Target. They run about $90 but you don't have do any of the scooping anymore. They only work regular clumping litter.
It is true that he higher quality pet food will produce different smelling poops. If you don't want to spend a lot on the super premium foods like Iams or Science Diet, you might want to try Purina One. I have found that it is comparable to the higher priced foods abd is about $4.50 for a three pound bag.