I intend to drive from Slovenia to Montenegro next year, mainly sticking to coastal Croatia on the way, but want to visit some islands as well with a vehicle.
I started in Split and I saw the ferries come in every day. I know they go at least as far as Dubrovnik, but not sure about where in between. There's not a lot of accessibility for cars in most ports for the smaller islands, so you're probably better off leaving your car in one of the major cities and taking a cruise of the islands in between. about 8 years ago