What medications are used for puppy megaesophagus and pneumonia?

Wow, this is quite a complicated case, so the answer will not be straightforward and is very involved. I'm assuming that you are trying to present an impressive report, but I'd recommend scaling this back, because the more complications you add, the more you will be accountable for.

There are a few fundamental things that I'd like to point out about your report that are already erroneous and may result in reduced points.

First, you need to understand the difference between symptoms and signs. Symptoms are what the patient is feeling and telling you. Examples of this are the patient feels tired, pain or dizzy. Since animals cannot talk, we can only base these things on observations (aka signs). This means that you can never truly refer to anything as a symptom in animals. They are all signs. Megaesophagus is a sign.

You should also be aware of the difference between ammonia and pneumonia.
Ammonia is a nitrogen-containing molecule and is often used as a cleaning product. Pneumonia is a condition where the lungs are diseased/inflamed.

If you have not been taught these concepts, then I doubt your instructor expects you to know what medications to give for this condition.

To make it easier, but still impressive, I would say that the pup has a persistent right aortic arch (PRAA) and that you need to place a stomach tube while he awaits surgery for the PRAA. Keep the SOAP simple to the level of education you are at. There is no way your instructor could expect you to know how to diagnose and treat these conditions. This is graduate veterinary level of work.

I know I still haven't answered you question, so I'll give you a few treatments below for pneumonia secondary to megaesophagus, which would be secondary to Mysthenia gravis. If he had this along with anemia and a stomach tube, then there would be no take-home meds, because this dog would need to be hospitalized.

IV enrofloxacin and metronidazole for the pneumonia
Oral (through the stomach tube) pyridostigmine for the Megaesophagus.
Blood transfusion depending on the severity of anemia

When dog recovers from pneumonia, it should go on oral prednisone for the Myesthenia Gravis.

I hope that helps and the project turns out well.