Forgive me for being blunt, but with only 24 days you are going to miss very many beautiful places in the Balkans. That's just the way it is. Are you contemplating seeing all the places on your list in 24 days? I think merely getting to them without actually seeing anything might take about that long. It appears to me that you have two 24-day trips there.
I have not been to Skopje, Pristina, Tirana or Medugorje. I believe transportation to at least the first three may be rather complicated and time-consuming.
Bucharest is far from the most interesting city (to me) in Romania, but transportation limitations often do require its inclusion in a Romanian itinerary. Ceausescu knocked down most of the interesting old buildings, so it takes quite a lot of time to see the remaining good stuff. (I admit that I was doing it on foot.) Just from the standpoint of physical attractiveness, I preferred Timisoara, Brasov, Sibiu, Sighisoara and Cluj-Napoca--all with cohesive historic centers that are easy to visit. Sibiu has a large outdoor folklore museum on the outskirts, with buildings brought in from all over the country. That's not really my type of thing, but it seemed well done, and it might appeal to you.
I thought the Maramures area in northwest Romania was extremely attractive (wooden churches, wooden gateways, Merry Cemetery, pretty countryside). I consider Maramures one of the best targets in the Balkans. Public transportation there is difficult if not non-existent, but it would be a piece of cake with a pre-arranged driver. Given your love of off-the-beaten-path destinations, I think Romania is a place you would really enjoy. The northeastern area of Bucovina, where the painted monasteries are located, is also worth visiting, but if I had to choose just one area it would definitely be Maramures.
Likewise, Sofia is not where I would go if I had only a little time in Bulgaria. I preferred Plovdiv and Veliko Trnovo. The coastal towns of Nesebar and Sozopol are also interesting, though very touristy in the way that beach towns often are. Not terribly convenient to get to, though. There's much more to see in Bulgaria, including the Rila Monastery, but my time there was limited.
While in Belgrade, I'd want to make a side-trip to Novi Sad.
I liked Kotor a lot, but it's important to be there on a day when there isn't a monster cruise ship in port. One of our regular posters has commented that Kotor is too similar to (and lesser than) Dubrovnik, which may be a fair comment if you're hitting both on the same trip. I loved Montenegro, though. It has many picturesque, distinctive towns (Herceg-Novi, Ulcinj and Cetinje included), and there's lovely scenery. The town of Budva is atmospheric but reminded me a lot of Kotor. The drive around the Bay of Kotor is not to be missed, of course,
I like Zagreb a lot for its historic center and good museums (2+ days for me). Don't try to see Plitvice (fabulous) on a day-trip from Zagreb. The crowding on the walkways is really severe during typical day-tripping hours. You need to spend the night before your visit in or near the park so you can get there early, ahead of the mob. Someone here said the park wasn't bad in the late afternoon, either, so you might try seeing part of it late in the day and the rest the next morning. It doesn't require a full day, so you'll be able to get started for your next stop reasonably early.
I also really liked Istria: Rovinj, Vrsar, Porec, Groznjan, Motovun.
I did not get to the Soca Valley in Slovenia, but it sounds like an area definitely worth exploring. I was happy to spend two days in Ljubljana, with extra time allotted for out-of-town trips.
I have no experience with private tours in Europe. The very good 2-day trip I took to Maramures was arranged by the Retro Hostel in Cluj-Napoca, which shows an extensive list of tours on its website.