Croatia Ferry and Flight Questions

Go on to: http://www.croatiaferries.com/ and type in your to-from points, check out the fares, then go on to: http://www.aferry.co.uk/specialoffers/croatia.htm and do comparisons.
Same for your flights..
Go to whichever airline you've found cheapest (EasyJet etc.), then go to: http://www.skyscanner.net/ and compare what you've found to pretty much everything else that's available.
Just one piece of advice on the Skyscanner site: It doesn't always have the most up to date fares on budget airline routes, so see who's doing them, see if there is an alternative price on Skyscanner and if not go directly to the airline and check it's latest fares out.

Indeed some restrictions on using Skyscanner as lenny says;
Consider Italian Pescara as your hub, then:
-Ferry Split to Pescara, see link above
-RyanAir: Pescara to Milan/Bergamo
-Bus Milan/Bergamo to Malpensa
There seems to be (there was) a possibility, direct to Malpensa but ..?..

The main ferry operator in Croatia is http://www.jadrolinija.hr/en/home. They offer booking for some routes.
Note there is also a bus from Dubrovnik to Korcula (bus takes a ferry).
There are a couple other operators that may be of use:
http://www.gv-line.hr/raspored.php?linija=3&lang=E
http://www.krilo.hr/en/

Thanks all for your help and advice, I really appreciate it. It looks like I am able to book the longer coastal ferries in advance and then the local ones right before the trip. Currently I am thinking about doing 3 nights in Dubrovnik, 1 night in Korcula, 1 night in Hvar, and 2 nights in Split. Does that sound reasonable?

I would skip Hvar in favour of two nights in Korčula. Both islands are beautiful, and you will be sorry to have to leave them the next day. It's better to stay put, explore more and enjoy the summer (lazy sunbathing, dinners al fresco...) than to be constantly on the road. Traveling in summer heat is hectic enough. Leave Hvar for next time.

@Nellstra

-EasyJet is the best option in this case - they fly direct from Split to Milan and they're quite cheap. Alternative could be another low-cost company - Volotea, but they fly between Split and Venice only.

• There isn't much choice when it comes to ferries from Dubrovnik. You can visit surrounding islands (e. g. Lopud) easily, otherwise you're quite limited with options. Good thing is that you can book most of those ferries from Dubrovnik to bigger islands in advance.

• Maddie's recommendation is good, plus Korčula is better connected with Dubrovnik so there's a better chance that you'll find a direct ferry or even bus between those two.

Thank you for the feedback and the sites!

Korcula seemed all around a more interesting place to visit from my point of view and I do like, as you mentioned AdriaticBlue, that Dubrovnik is closer.

I will also check out Volotea as I have never heard of them until now.