C 1857 the Catholic orphanage for boys at Agra was St Paul’s, although the Catholic boys’ school was St Peter’s.http://books.google.com.au/books?id=j2MtAAAAYAAJ&pg=RA1-...
It does seem somewhat unusual that your ancestor was brought up in a Catholic orphanage, if in fact he had not been baptised Catholic. If you look at the actual record above, the transcript of which are quoted, it may indicate (directly or indirectly) into which religion he was baptised
The description of his medical training etc is suggestive of that of an Apothecary, called from 1894 an Assistant Surgeon.
For details, see the FIBIS Fibiwiki page Apothecaryhttp://wiki.fibis.org/index.php/Apothecary
One of the sources for tracing an Apothecaey are editions of Thacker’s Bengal Directory, or from 1885 Thacker’s Indian Directory.
There are some online editions of Thacker’s Bengal Directory 1875-1884 (broken range) which may assist, see the FIBIS Fibiwiki page Directories onlinehttp://wiki.fibis.org/index.php/Directories_online