Why is your puppy living in the basement?
I think you need to research Raw diets. From what I have understood variety is the best...eating chicken every day may not be so healthy.
I would not be surrounding your dog with harsh chemicals such as incense and febreeze. It sounds like your basement is not very well ventelated...this would not be good for your puppy to be breathing in.
You have four
small windows for ventilation...I doubt this is enough to allow for proper air flow. Perhaps your dog stinks because he is living in the same dingy air? Heat combined with stale air and feces/urine is not a good combo. The heat bakes the waste smell into the air. Does your dog go outside to potty? Maybe you could get an air conditioning unit to help bring fresh air in.
I doubt its anal glands...you would know
!! The smell would make you want to vomit.