Regarding the bus situation, the deal is that there are at least three different official bus stations that I know of for inter-Nicaraguan trips. Mercado Huembes for points South, Mercado Mayoreo for points North and East and Mercado Israel Lewites for points Northwest. So if you are coming from the South but heading further afield, you likely need to get yourself to the appropriate market. Taxi is really the only way to go between the different bus stations, especially if you have baggage and such. Another reason to travel light!
(There are also the areas where TicaBus/NicaBus leaves from for international trips and “la UCA” for minivan expressos to most anywhere.)
As for Granada to San Juan del Sur, see if you can find a bus that goes to Penas Blancas (the border/la frontera). They would drop you off at the turnoff/empalme to SJdS, and typically a local bus would come by or if you are lucky be waiting for you. Alternatively there are always taxis at the empalme to take you to SJdS.
I’m not up on whether or not minivans leaving from SJdS would go to “la UCA” where as you rightly say, expressos to Leon leave from. The buses and expresso vans I am familiar with end up at Mercado Huembes and from there you would need to taxi to la UCA for minivan or Mercado Israel Lewites for regular buses.