Hi,
I know it's frustrating to have a young dog with so many problems already. You're right, mucous in the stool is not a normal condition. It indicates a problem with the lower intestine (colon). Sometimes, dogs have a bacterial overgrowth in their stomach, especially if your dog has been on antibiotics. Your vet did not likely test for this if they did a routine fecal exam which tests for parasites. You should ask your vet to do a fecal culture/smear and potentially send it off to folate / cobalamine testing. They should also do a Giardia test as Giardia is difficult to see on a routine fecal.
As far as treatment is concerned, the first thing I would want to do is to put your dog on a probiotic which is designed to replace the normal bacterial flora present in your dog's stomach. You can purchase acidophilis (live/active culture) at a health food store, or there are several animal products available on line. You need to make sure it's "active".
I would also suggest switching to a whole foods diet -- not a commercial brand. Some dogs are sensitive to the preservatives in dog food. There is a great book called "Dr. Pitcairns Guide to Natural Animal Heatlh" that outlines diets for dogs which are well balanced and free of allergens.
Another thought for you -- there are many veterinarians (myself included) who practice homeopathic medicine. This is a type of medicine which views your dog's symptoms as a whole, not each disease separately. The remedies are safe and natural and in many instances, highly effective. A consultation for this type of case is beyond the scope of this forum, but can be arranged either in person with some vets or via telephone. Please let me know if I can refer you to someone who does this type of work. I hate to see puppies this young on chronic antibiotics.
Please let me know if you need more information.
I share your concerns and am glad you have sought out help. I strive to provide you with excellent service. If this information has been helpful to you, please Accept! Bonuses are ALWAYS APPRECIATED.