Tom, there are some good hydraulic shops around the area might be able to advise you. Carter's in MHC comes to mind. There is a place in Raleigh I have bought parts from that serves the heavy equipment market, name escapes me at the moment, but there are a bunch of them up there. You could call one of those places and perhaps they could walk you through how to figure out what you have. Edit: name of the place is Motion Industries, they were very helpful finding an obscure part.
Yes, pumps come in all sizes. What is used on your stern thruster is quite different from that used on say, Caterpillar D9. My Naiads have a Vickers pump that is only big enough for that purpose; I suspect, but don't know, that the same applies to your thruster.