I went down as far as Dubrovnik in september 2006. Don't underestimate how far you'll be riding - I did 4500 miles in total.
Went down via Austria and Slovenia and back up via the Dolomites, Switzerland, and the French Alps. You could do the trip in two weeks, but you'd be riding non-stop with little opportunity for taking in the local sites. I allowed 3 weeks which gave me enough time for a few days on the beach on the Croatian islands, a day to see Dubrovnik and an extra day in the Dolomites.
I did think of taking in Mostar on the way back up, but the weather wasn't great. Your insurance will cover you for all of the EU, and they'll usually include Croatia as well. Any further south than this and you'll need to speak to your insurer, of more likely buy it locally.
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