The journey from Ljubljana to Pula on Slovenia Rail shows only one train from Divača to Pula and the journey from Ljubljana by bus - although there is a connecting train from Slovenia.
As Slovenian Railways informs us, trouble there is because of "Zaradi sanacije posledic žledu", but perhaps it will be fixed and instead of substitution buses in October there will be trains already. But even if not, bus is 100% "coordinated" with the train, so nothing to worry about in terms of change from one to another. As an alternative you can also take morning or evening train to Rijeka (btw, nice place itself) and then Croatian domestic bus to Pula from there. Or direct bus from Ljubljana to Pula via Koper, Portoroz
Pula-Plitvice lakes-Split: although you can reach Plitvice lakes by bus, but perhaps here your best option would be car rental, it will save you quite a lot of time and allow to see many interesting places (e.g. hire a car in Pula or Rijeka, then drive along the cost till Senj, turn to Plitvice, while from there back to the cost and through Zadar-Sibenik-Trogir to Split.
Split-Hvar &
Hvar-Dubrovnik: pretty much your only choice here is taking a ferry (unless you want to come back to Split and take a bus to Dubrovnik), but it's very picturesque journey, thus hardly anybody would complain about such "only ferry" option. With Split to Hvar there are more options regarding companies (you can read through
http://europetrainsguide.com/forum/index.php/topic,782.0.html ), while with Hvar to Dubrovnik unfortunately there is not much choice - Jadrolinija canceled their ferry on leg Rijeka-Split-Hvar-Dubrovnik, so it seems that only one company serves the route now.
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