4 days in Morocco in late September

Avoid these days. You will come in Ramadan and you will be culturally shocked. Also you'll have great problems to eat comfortably once you leave the bigger cities like Casablanca and Marrakech.

Yes you can take a ferry from Algeciras to Tangiers, then take the train to where ever you want to go next. I would suggest Fes and Rabat.
I wouldn't avoid Ramadan, but make sure you have some snacks & drinks to you can discreetly partake of in your rooms - Moroccans eat at night and fast all day during Ramadan - and that includes refraining from beverages as well. More and more restaurants close for the entire month and use that time to repaint, etc., but in the larger cities you can find McDonalds and a few other places open during the day, and cafes open at night.
Ramadan is an amazing thing to witness, there's lots of entertainment at night, everyone is out walking around between meals.
In Ramadan, travelers are exempt from the fasting, but Muslims are expected to make it up some other time during the year, so many just prefer to do it when everybody else is doing it.
You, as a non-Muslim, aren't required to fast, but it does make it easier to just go with the flow, you will be admired for trying, and who knows, maybe you'll be invited to break the fast with someone in their home.