tours from cuise ship to Spain and Portugal

You might check CruiseCritic.com.

They might better cover shore excursions there.

http://www.palaumusica.cat/en

Am confident you shall receive ample guidance on places to visit so I shall focus on an experience in Barcelona which many miss.

Check out the above web site and consider the following:

• this is a fabulous place to visit simply for truly unique architecture (and I use the word "unique" deliberately)

• attend a concert, regardless of music selection, and you will find yourself sharing an experience highly valued by locals. Hence, this is a terrific opportunity to create a memory well beyond a "been there/seen that" experience.

From Malaga I would go to Granada and encourage you to spend the night there. Yes, you are paying for a hotel while leaving a cruise cabin empty, but the Granada menu of opportunities justifies the expense.

From Cadiz I would go to Seville and also spend the night. Same rationale.

I'm glad to hear that you have two days at some stops. We don't recommend any really comprehensive shore excursions or tours because you can easily see these cities using public transportation. Many of them are well covered in Rick's Spain guidebook, plus the Lisbon snapshot. Of course shorter bus or walking tours are recommended in those books, to get an overview of a new city, but usually not to organize your whole day.

Train or bus options run pretty frequently between the alternate cities that Marbleskies suggested.
Direct trains from Cadiz to Sevilla run at least every two hours and take 1 hour 45 min or bus travel time is similar by http://www.tgcomes.es/horarios_13.htm. Trains from Malaga to Granada are less frequent and require a connection, while bus is more frequent and direct, by www.alsa.es. There's no deadline to buy train or bus tickets. How to Look Up Train Schedules and Routes Online gives you the DB train schedule link and tips for using it (but does not sell Spanish tickets).