The Doctor uses Astronomy for his medical treatments "For being grounded in Astronomy...worked on the images for his dependent." "The cause of every malady...moist or hot" refers to the fluids of the body which had these four qualities. Sickness could be caused by an imbalance.
The Doctor is in league with the Apothecaries (druggists) who sell the drugs that he prescribes. "And each made money from the other"s guile". It is fair to assume that the Doctor got some sort of payment from the Apothecaries.
The Doctor is in good physical shape because he eats well "No superfluities for pleasure". He is wearing "Blood red garments, slashed with bluish gray and lined with taffeta (silk)."
Pestilence are contagious diseases, usually fatal.
The Doctor "had a special love of gold."