Unlike most in the RS forum, I have been to Bosnia-Herzogovenia (Mostar, Sarajevo) and Serbia (Beograd, Novi Sad). I have not been to many outlying towns.
Good to know that, and I thus believe that your constructive recommendation will be useful for me.
1) You have 4 days and 8 cities for Serbia, 4 days and 5 cities for B-H. That means that every single day you will be driving for 2-3 hours (min), taking 1 hour to unpack, and then have time for whatever tourism you are interested in. That's not a trip I would enjoy. What is the point of your trip?
The list of cities/places is not a conclusive one. I came across these during my research and listed them down for further opinion from this forum. I am open to suggestions to delete/modify these. As I said in the opening paragraph, "We are interested in villages, mountains and natural scenery. Museums, memorials and cities do not excite us much". So that's the purpose of my trip.
2) You should cut your trip to at most 3 locations, or find a way to add 30 days for the number of destinations you have. Even 38 days is too few for 13 destinations.
As they say, YMMV. No number of days are ever enough for any country. You may spend 30/38 days and still leave unsatisfied. For me, time is limited - I am not a backpacker and have to return to my job. I am trying to maximize the 8-10 days vacation that I have, hence seeking suggestions on which places should be visited to get a flavor of these two countries.
3) Do you speak Serbian or read Cyrillic? Serbia is very underdeveloped touristically, and you are less likely to find English speakers in small Serbian towns. Mostar, Sarajevo, Beograd, Novi Sad - you will find English speakers. The smaller towns, less so.
I neither speak Serbian nor read Cyrillic. Is that going to be a deal breaker to even plan a trip in these countries? I have traveled to many countries without knowing the language and it didn't pose any challenge. As for directions, I am relying on Google Maps (as I have done in the past), to be supplemented by asking locals, if the need arises.
4) Begin with a planning map that includes Sofia. Put each city/location in, and the travel time (from google maps). My estimate of 2-3 hours may be low. Some of these places are doubtless remote with possibly bad roads.
That's exactly what I did. I plotted the list of places on Google Maps, got the driving time and distance and that's the sequential route (indicated by arrows) that you see in my opening post.
5) One approach that might work would be to set up in a base and do day trips.
I did think of that, but it doesn't seem possible because both Belgrade and Sarajevo are pretty far from other places. Day trips wont be feasible or will just be extremely tiring.
Unless of course you can suggest day-trip worthy places near Belgrade and Sarajevo? By that I mean 1-2 hour driving distance one way.