I did a three-week trip to Croatia, Slovenia, and Bosnia in May 2014. I got tons of advice and found it very hard to settle on an itinerary, as there are so many places worth seeing, and everyone has an opinion, and you can't go everywhere.
The good news is you can't go wrong. The fact that there are so many places worth seeing means that it is very likely that anywhere and everywhere you go will be great!
Dubrovnik and Korcula are not redundant. Korcula is much more laid-back, with a relaxed island vibe and a ton of charm. Dubrovnik is more bustling and visually impressive. Three nights there will give you opportunities for day trips or activities like kayaking. You could travel to Kotor for a day, and Cavtat is not far and can be visited by a short boat ride or by bus.
I second the advice to get to Mostar, since you'll be very close when you're in Medugorje.
I didn't get to the horse farm or to Postojna Cave when I was there. I do highly recommend hiking the Kobarid Historic Trail. Also, heading out of Kobarid toward Istria I stopped at Tolmin Gorge. It was well worth the visit. (Vintgar Gorge, near Bled, was closed when I was there due to damage caused by severe winter weather. At the TI in Kobarid I was told that Vintgar is actually nicer than Vintgar.) I also stopped at Škocjan Caves, and while it was impressive to see, you have to visit it on large group tours. I felt like we were being herded through like sheep and our guide was not very pleasant. Also, photos are not allowed inside the caves.
When you're in Rovinj and taking day trips, my favorite small town was Grožnjan.
Just don't spend too much time and effort second-guessing yourself. You'll have a great time whatever you decide.