looking for sage advice

I like to keep things simple. Two weeks in Croatia and four weeks in Spain would be marvelous in my book. The other option are indeed endless--if you did not want to fly, you could look at the train lines to see some of the possibilities. Or, look at a website like Skyscanner to get an overview of flights from Split (or other Croatian airports) and to Sevilla/Malaga/Jerez (the three airports I know of in Andalucia)/Madrid.

Just be aware that much of Spain is very hot in the summer, especially Andalusia. You might consider the white villages. Grazelema is at higher altitude and tends to be cooler. We stayed at La Mejorana, which had a lovely setting and a beautiful pool. It also was very modestly priced. Maybe you'd want to spend time in the Basque area of Spain, where it will be cooler. Also, I contemplated a trip to Croatia for August and followed their weather for a few days. It was quite hot, too. Maybe you would want to consider a stay in the mountains between your stays in Croatia and Andalusia. You could consider the Dolomites or the mountains of Austria.

We really need much more information about what you want out of the trip and any parameters you have (weather--what months?, transport/activity preferences, etc.)--but lucky you to have a whole month and a half to figure out! Google Maps has come a long way and will give you an instant overview of some options.
Thoughts to consider:
Have you been to Croatia before? Do you want to see a lot of the country, or just visit the friend in the Trogir/Split area?

Ditto Spain--will you be spending time with family in the country. Is the heat an issue (I would not worry about June unless you have health considerations, but in July and August I would also limit my time in all but northern Spain).

This site works a lot better responding to your proposed travel schedule than trying to develop a travel schedule for you with min information. We are not travel planners but can offer "sage advice" once we know what you would like to do. It would even be helpful to know where you are traveling from. We are good but mind reading is not one of our best features.

If this was my trip, simply to save time, I’d fly. Out of curiosity, which part of Andalucia does your daughter live in? For your time in Spain, I’d rent a car since there are some very nice off the beaten path sights not easily accessible using public transportation.

Unless you want the trip to be rushed, I don’t think that you have time to see all of Croatia in 2 weeks. In this timescale, you could start in Dubrovnik for a few days then head to Korcula for 3 nights and/or the island of Hvar for 3 nights (I would stay in Stari Grad, not Hvar town), then a few days in Trogir (visit Split from here). Plitvice could also be done from here, but it’s a long day trip as you need to be there early to avoid the crowds. It maybe easier to get flights from Zagreb than Split to Spain, so have a few nights here too.

Alternatively, stay in Trogir then have a week in Istria then fly to Spain.

Look at seat61.com as a guide to European rail travel. There are no trains to/from Dubrovnik.

I would fly in and out of Spain, and go to Croatia for the side trip at the beginning; after a couple of days in Spain to get over jetlag. That way it might make for cheaper flights from home and returning home if they are from the same airport.
Fly to and from Croatia.
Have your car in Spain when you return there.
Also, a Eurail pass is rarely worth the money, as it might be cheaper to buy train tickets as you go, if you plan to use any trains.

Regarding your flights: if an open jaw itinerary is too expensive you might consider flying R/T from New York into one of the major European hubs (London, Frankfurt, Amsterdam, etc) and then availing yourselves of cheap flights within Europe to get to Dubrovnik, Andalusia (Malaga?), from there and then back to your hub to catch your return flight. Scheduling a day or two at your hub city would allow you to explore it at your leisure and maybe shed a little of your jet lag before pushing on.
Can explore schedules and costs on Google flights at https://www.google.com/travel/flights.
Might be a much more cost-effective option for you than an open jaw.

Eurail is one of the worst sites for train information. They basically sell passes. Instead use:

http://www.bahn.com

But I would forget the train.....from Zagreb to Seville would take 45 hours and seven changes. In other words......fly.

As for cars, see if the rental companies will let you pick up on Croatia and drop in Spain. Also be aware of drop off charges.

First, suggest flying into Split for your start of the Croatian journey. Then depart from Dubrovnik for trip to Spain.

Trogir is small and quaint while placing you on the door step of Split and several other potential destinations. I am attaching a trip report with the focus being on potential island hopping destinations. Upon our return to Croatia we will rely upon the excellent ferry system to continue our exploration of the coast. We enjoyed being on a ship to explore the seaside ports and gained an additional sense of perspective by using a mode of transportation common to the realm, but not so much in the USA.

https://community.ricksteves.com/travel-forum/trip-reports/a-small-ship-cruise-in-croatia-october-2019

There are inland destinations to discover such as Plitvice Park and Krka Park. Renting a car to access these destinations is relatively easy and inexpensive to accomplish. Do your research on Plitvice as we recommend an overnight stay to fully enjoy the area. Accommodations book fast so making a commitment to visit is important. You can travel from Trogir to Plitvice and back then return the car to continue the journey via ferry. Krka can be a day trip due to ease of access and proximity to Trogir.

We recommend three nights at the end of your two weeks in Dubrovnik due to a variety of experience options.

Our first trip to Croatia was for 10 days and we plan to return to spend at least ten more days in the area. We found a large menu of experiences left unexplored, the people are great and less expensive compared to other journeys. So we encourage you to stay within Croatia and then travel to Andalucia where we are envious of your ability to spend a month. Yes, it is "warm" in June, but Vermouth and Sherry greatly assist with tempering the climate.

Safe travels!

Agh! Can't believe I forgot to mention the excellent ferry services connecting towns and islands among the Croatian coast. These ferries are easy to research, easy and relatively inexpensive to use and the form of transport we intend to travel upon our return.

Now that we have the huge gaps filled in (way to bury the details, lol), by all means fly from Croatia to Spain. You could eat weeks on a train. I think your best bet will be concentrating on the Croatia and Spain parts as separate itineraries, and just scout out the best place to fly between them.
I would have started in Spain and ended in Croatia for weather reasons, but unless you wanted to swim, mid-May should be nice in Croatia. The sea is rather chilly until late May.
From NYC to Croatia, you should be able to fly to Zagreb, Split, or Dubrovnik with one stopover.

Op said they live in New Mexico, so they are familiar with heat......

For the croatia part of your trip you will need to do a little research. Trogir is an hour ferry ride from split or about the same on the bus. We just prefer any mode of transportation over a bus. Split is 3 hours from dubrovnik, one hour from šibenik, close to Krka national park. In other words, there are many places to see which are closeby. You can go to Croatiaferries.com and see all the connections. It’s usually very difficult to park along the coastal cities, but there are lots you can park a car in. When we drive from our base in Rijeka, we drop off the car in the first city we are visiting and ferry around from there. This september our itinerary is Rijeka, drive to dubrovnik with lunch stop in Šibenik, drop off car, ferry to korčula, ferry to split. You get the idea. Just choose the places you want to see, check if they are a day trip or if you need a night or two, then figure out the transporation. Sometimes places we choose are because of the ease of transporation. Every island, city, town has its own charm, you won’t be disappointed.

thank you every one for your excellent advice and for helping me wit the learning curve on travel forums:)

We are going to keep it simple and just concentrate on Croatia and Spain ( how lucky we are!)

We are going to fly in and out of Madrid and then fly to Dubrovnik after a few down days in Madrid. We are now exploring taking a cruise up the coast as suggested and making our home base at our friends apt on Ciovo Island, using them as our tour guides ( they live in Trogir) and just seeing as much as we can in 2 weeks, along with enjoying our friends and their family. We will then fly back to Madrid from Dubrovnik and rent a car for the remainder of our visit and travel down to Vejer de la Frontera where our daughter lives and which is familiar territory for us.

Thank you all for helping us "uncomplicated" this trip. We are feeling much less anxious and very excited.

Karen and Bill