30 Days in Croatia

Transport preference?
You have it lined up really well to arrive in south in September (great swimming temps) and end in the north in October (fall color, truffle season in Istria), so you just need to pick the islands that appeal to you the most. Really all of the islands have something to offer--though you will hear favorites (for the record, mine was Vis!)
I know nothing about diving, but the tourist agency can be of help if you don't get any feedback on that.
https://croatia.hr/en-gb/outdoors-and-active-holidays/diving
https://www.scubadiving.com/where-to-go-scuba-diving-in-croatia
https://www.divessi.com/en/mydiveguide/destination/croatia-9750157
The transport along the coast was really easy to me--convenient and adequately comfortable buses, catamarans among the islands. For Istria, a car is needed for the interior towns. You can easily do a rental on an island if you want to explore widely--so I think a hodgepodge approach is best for transport.
See the Krilo and Jadrolinija websites to get an idea of the routes.
I think I've blathered on enough for today, but happy to answer any questions I can.

The water is so clear we could see the bottom from the dock, I'm sure you both will have a wonderful time. J

30 days is a good journey. You should take advantage of it. If you havent booked your flights yet, you might turn it around and fly into Zagreb and out of Podgorica. I only say that because this is a Croatia adventure for you and i thought it might set with your mind a little easier to break the boundaries at the end of your trip than at the begining.

I have been to Croatia a few times and to be honest with you, unless my goal was to chill on a beach a lot (which isnt an altogeather bad idea at my advanced age), I would have trouble staying busy in Croatia for 30 days. Good news, Bosnia & Herzegovina (BiH) and Montenegro are at your service. 4 to 6 days in BiH and 5 to 7 days in Montenegro would round out the trip nicely. Podgorica, the capital of Montenegro, has an airport that is at least as well connected as Zagreb. Its where I fly into when I go to Croatia or to Montenegro (I live in Budapest).

By they way, there are a couple of PADI places in Budva, Montenegro. I will be visiting one in May. I spent 20 years diving then went through a 30 year period when it ws forbidden ... time to restart .... means relearning so a resort course in Belize last year and another this year in Montenegro till i get the time to do it right. Still, it gets me wet.

I bet you have researched the heck out of Croatia so I will leave that one alone and just push the Montenegro and BiH extensions in PMs to you or the posts will get very long.

Thanks everyone for the input. I’ll post more as we finalize plans. One question. I have been searching online to see if there is some sort of ferry or catamaran pass that allows you to get on and off at different islands as long as you continue in the direction you start? We’ve used them in Greece between islands and also something similar on buses in Australia.

We were considering catching the first ride from Dubrovnik and heading north, stopping at a few islands for a day or two on each and then back onto the mainland. Most of the ferries I saw were just back and forth between two, or sometimes three locations.

There is no ferry pass that we ever read about or saw advertised at any TI offices.

If anything like that exists (it did not in the past, just point to point sales), it will be on one of the websites I mentioned, as they are the primary providers. You do have time to do a small cruise, so you could look into that if you wanted to move that quickly. Sometimes the catamaran schedule facilitates it, sometimes not. I never found it difficult to move among the islands myself and I prefer that so I can explore the islands more. I recommend giving each island stop more time than just a day or two, allowing you time to take in the landscapes as well as the secondary dwelling in each (aside from the main town that each island typically has). Maybe you have extensive plans for the mainland later in the trip, but without knowing that, with 30 days you could stay as long on islands as you want, nice “problem” to have!

I lived in Zagreb from 11/22 - 05/23. Most boring city I have lived in, between Prague, CZ and Split, HR. From what Google Maps shows, the main cathedral is still closed. Not a lot to do there, so I wouldn't spend much time there.