Itinerary recommendation for Self-travel. Croatia/Bosnia

In my opinion both Mostar and sarajevo are way more interesting than Zagreb. I would take 2 days off Zagreb and add a day to Sarajevo and a day to Mostar.

Agree completely with #1, your itinerary seems a bit rushed as it is, and you should not try to add yet another destination to your list. While Zagreb is a pleasant city indeed, I think it makes more sense to spend an additional day in Sarajevo and/or Mostar - these cities are less "regular", or more "exotic" if you like, than Zagreb.

An alternative to the Sarajevo-Zagreb train could be to take a bus from Sarajevo to Banja Luka on the Travnik-Jajce road (check the map), and board the train to Zagreb in Banja Luka. I think this is a much more attractive route.

For your extra days at the end of your trip you can visit the area northwest of Zagreb dotted with castles or/and baroque town of Varazdin, easily done on a day trip. Check the tourist info office for details. In every of the places you plan to visit you could easily spend more days, but Zagreb, if less exotic, is the largest and definitely has more to offer than the rest combined. Anyway, your trip will show you the great diversity of landscapes, cultures and peoples of the region.

I'd spend the extra day(s) in Montenegro. Instead of the day trip stay at least 1 night in Kotor.

Instead of taking the bus from Mostar to Sarajevo I'd take the train. It is one of the most beautiful rail lines in the world and this might be your last chance to do it, because the future of railways is very uncertain in Bosnia.

http://www.balkanology.com/overview/article_scenicrailways.html

http://www.blockstelle.de/hr18/index.html

As someone else has said, the train ride is more scenic. It departs from Ploče, Croatia. It is an old train but an interesting experience. You could bus from Dubrovnik to Ploče, perhaps with a stop in Ston to see the salt flats. There are a couple of buses involved, just ask at the station when you get to Dubrovnik for help coordinating. You could also take the bus Dubrovnik-Mostar as planned, and do the train on the Mostar-Sarajevo leg. There is always construction on some part of the rail lines so don't be at all surprised if the train suddenly stops and you're ushered onto an old bus, driven part way and put back on the train. It's sort of hilarious. And take snacks.

As to the itinerary, I would leave it about as is. That time of year there are hardly any tourists left (which is wonderful) and you really can be flexible as there will be plenty of room on public transportation and private accommodation available. No need at all to get hung up on an exact plan or travel/room reservations. If you love Sarajevo, stay an extra night. If you get to Zagreb with a few extra days on the end as scheduled, you can really explore the city. A lot of people short-change Zagreb, when actually there are some great museums, food and cafe culture, open air markets and photography opportunities. It contains a quarter of the Croatian population and is much bigger than all the other places on your list. You can take the bus to Samobor for a nice afternoon, do a short hike in Medvenica park north of the city, catch a show, whatever. You can even easily take a day train-trip to Lljubljana, if you're up for more time on a train at that point!

One more note - in Oct it will be chilly at night inland, Sarajevo around 7C (low 40sF), about 17 during the day. It will be a little warmer in Zagreb but not by much. The difference being in Sarajevo a lot of people use coal or wood for heat and the city is basically in a bowl blocked by mountains. Plus literally everyone in Sarajevo smokes (hardly any no-smoking places indoors), like here in the U.S. in the 50s or something. Plan on smelling like a chimney if there when there's a cold snap. Be sure to check out the old guys playing chess in the park, they're great. Large chess pieces on the ground and the bystanders telling the two competitors what they should be doing the whole game.