Hi Dave,
I recently returned from a similar trip, so I'll give you my itinerary, which may be of interest:
Ljubljana (2 days)
Bus to Piran, which I count as one of my favourite places in all of Europe. It really is an incredible place and totally unknown outside of Slovenia. We stayed here for 3 days.
Bus from Piran to Rijeka (via Koper), which was a beautiful ride. Rijeka isn't a particularly attractive city, but we boarded the Jadrolinia ferry which runs down the Croatian coast, stopping off at numerous places including Split, Zadar and Korcula, all the way to Dubrovnik (and thence Italy). It is however only weekly. It was very cheap, but we slept on the deck (which isn't recommended - and demanded a lot of Croatian vodka to see of the cold).
We skipped Dubrovnik, as it is very expensive and terribly touristy. We took a bus from its very orderly bus station to Mostar (about two hours), which is a truly fascinating city. One day is enough to see it, but try and get away from the tours; it is perfectly possible to do it independently.
We took a train to Sarajevo, which was about three hours and cost 5 EUR each way [sic!]. Two days in Sarajevo, which is a very attractive city, though still visibly reeling from the recent conflict.
We then took a bus down to Kotor, via Mostar and Dubrovnik. Kotor is a beautiful place and well worth a visit. We stayed for three days, which was more than enough, though not too long.
From Kotor we continued down to Bar, which is unremarkable apart from its completely-unknown mediaeval ruined city, which was astounding. Ulcinj is supposed to be much more enjoyable. We stayed in beautiful hotel with Satellite TV and AC for 10 EUR a night.
From Bar we took what is surely the most breathtaking railway journey in Europe, all the way to Belgrade (timetabled to take around 10 hours and costing 25 EUR).
The former Yugoslavia was gobsmackingly beautiful and I can't recommend it enough. Have a great time!
Mark