So far as soiling her loft try moving it to the other end of the cage and adding a fluffy bed.
Here is some info about her possibly eating her poop:
Coprophagy is the term for eating poop, it is a frustrating habit for owners but it is not harmful to the puppy. If the puppy had intestinal parasites you can make a point that he reinfects himself but your veterinarian will be sure that he is free of intestinal parasites and suggest products to prevent that from happening. There are several products that you can add to his food which will usually break the habit and many puppies outgrow it anyway. These products work by changing the chemistry of the poop and rendering it unattractive. Some examples are: Forbid, Deter, multiple herbal preparations.
The products available to help discourage your puppy from consuming poop are available in powder, tablet and soft chew forms. The principle behind these products is to use enzyme action to chemically alter the feces inn hopes that it creates a change in the smell and attractiveness of the poop. I wouldn't consider one of these products to be superior to the others in fact I have found that a product that works very nicely for one puppy has no effect on other puppies. Pick a place to start and be aware that the product has to be used at least a couple times daily and may need to be used for 2-3 weeks. If your first choice fails move on to another. Before all the products for puppies were available a sprinkling of unseasoned meat tenderizer (source of enzymes) often worked.