Coccidia can be in their system dormant and activated by stress. There are no antibiotics to kill the parasite (but they do keep it from reproducing). You may need more than one round until he can get rid of it. Like kennel cough the dog's immune system must overtake it on its own. Look at getting an immune system booster supplement to give him.
Even good foods sometimes don't agree with some. I feed Nutro Ultra dry with no problem, but the Nutro Ultra canned caused vomiting, but not the Nutro canned for sensitive tummies with oatmeal.
Hopefully, the undescended testicle will still drop if he is under 5 months old, but usually it's not that big of a deal (a little more expensive surgery and a bigger incision). I would definitely recommend the neuter though because it is more likely to develop cancer and is passed on genetically to offspring.
Here's a link on comparing reverse sneezing to collapsed trachea you might find helpful - choose hypoglycemia on the left and then collapsed trachea.
http://www.glassyorkies.com/
Also thumbs up to your vet on holding off on the vaccine.