I did a similar itinerary this past Spring, during shoulder season and private accommodation was the best way to go in terms of pricing and we had some great locations. Most often there are people who are just waiting at the bus stations and ask as you get off the bus if you are looking for a room, if this doesn't happen you can usually go to the nearest travel agency and ask, they tend to have a list of people they call. Only in the smaller coastal towns did we have a problem as it wasn't high season so rooms were still 'closed' until things picked up.
If you did go this route make sure you get all information before going with someone because once you're in their house it can be hard to turn back...private or shared bathroom, are towels included, how close to center/beach, etc.
Also, there is a great place in Split called Hostel Nikolla, which has a nice kitchen, free computer, outdoor dining area and the nicest family runs the place.
Some of my favorite places...Plitvice Lakes, Rovijn, Korcula(if you're hitting the islands)