12 days in Madrid/Andalucia region

Is Day 1 the day your fly in from the US or Canada? If so, you really hardly have any time in Madrid, because you are likely to be a zombie that first day from lack of sleep and jetlag.

I think you're moving much too fast, checking into hotels 8 times over the course of 12 days. That wastes a great deal of time.

I would definitely drop Tarifa/Tangier. Morocco's great, but a day-trip to Tangier is not so wonderful, and you really don't have time for that.

To further reduce the check-in/check-out part of your trip, I'd plan to head straight to Cordoba on your arrival day, consolidating all your Madrid time at the end of the trip. This will probably mean paying walk-up prices for your rail ticket to Cordoba, but it's a good use of a day when you will be not very alert anyway.

If you make enough changes that you feel you have some extra time (I think Seville, Cordoba and Granada will absorb it), you can consider a day-trip from Madrid. Toledo and Segovia are both worthwhile, and you don't need to pre-purchase the rail tickets.

I would probably switch your Tarifa and Ronda stops, but I always have a rental car. Or you could switch the itinerary around a little and do:
Madrid - Granada - Nerja - Tarifa - Ronda - Sevilla - Cordoba - Madrid
Seems that would eliminate any backtracking, but of course would be dependent on train schedules. The roads in Spain are good and well marked. I usually only use Garmin to get out of towns heading in the right direction. Parking in Sevilla can be a pain as is parking in most cities, so you could still turn in the car in Sevilla and take a bus to Cordoba.

Thank you for the suggestions! So, if I drop Tarifa and day trip to Morocco, and went straight to Cordoba after flying into Madrid from the U.S., I could possibly do this slightly-less-insane schedule. Adding extra nights in Nerja, Ronda, and Seville.

9/17: Travel day from U.S. to Madrid, train to Cordoba

9/18, Day 1: Cordoba

9/19, Day 2: Cordoba to Granada

9/20, Day 3: Granada

9/21, Day 4: Granada to Nerja

9/22, Day 5: Nerja

9/23, Day 6: Nerja to Ronda

9/24, Day 7: Ronda

9/25, Day 8: Ronda to Seville

9/26, Day 9: Seville

9/27, Day 10: Seville

9/28, Day 11: Seville to Madrid

9/29, Day 12: Madrid

9/30: Travel day from Madrid back to U.S.

Personally I would drop Nerja in favour of extended time in Madrid, allowing for day trips to Toledo and Segovia.
Córdoba (2N)
Granada (2N)
Ronda (2N)
Sevilla (3N)
Madrid (4N) - with days to Toledo & Segovia

Thank you, djp_syd! I have been trying to decide what to cut out so that I am not running around like a crazy person, checking into hotels every other night. We live in Colorado, USA, and haven't seen the ocean in many years, so that's why I was trying to work in Nerja, or some coastal place to at least enjoy some kind of ocean. I know there can be other opportunities in life to see ocean, so I may drop Nerja to spend more time in other places. I wish I had 6 weeks (or a lifetime) to spend in lovely Spain! :)

My agenda is looking like this as of now (after I clued into the fact that I will lose a day of travel to get to Spain from the US!):

Sept. 17-18: Travel to Madrid, arrive 9/18 5:30 pm, stay in Madrid 9/18 night because I'll be a jet-lagged zombie (I have read it takes 3 hours to get through customs/security?)

Sept. 19: Madrid

Sept. 20: Madrid to Cordoba (AVE)

Sept. 21: Cordoba to Granada (ALSA, 3hrs?, can we stop in Antequeras?)

Sept. 22: Granada

Sept. 23: Granada to Nerja (rent car)

Sept. 24: Nerja (car)

Sept. 25: Nerja to Ronda (car)

Sept. 26: Ronda (car)

Sept. 27: Ronda to Seville (stop through Arcos)

Sept. 28: Seville (drop off car)

Sept 29: Seville to Madrid (AVE), 3hrs

Sept. 30: Travel day from Madrid back to U.S.

This is still many times to check into hotels - seven out of 11 full days in country. Gah! I know it's too much. I need to cut something so I am not exhausted after my vacation. I also wanted to try to get 3 nights in Seville. Can I make some of the "White Hill Towns" day trips? There are so many beautiful things to see. Halp! :)

Perhaps squeeze Cordoba a little first up, allowing more time for Madrid at the back end.

Sept. 18: Arrive Madrid (1N).
Stay one night near Atocha station.
Sept. 19: Make an early start from Madrid to Cordoba (1N)
Sept. 20: Cordoba to Granada (2N)
Sept. 21: Granada
Sept. 22: (pick up car) for Granada to Nerja (2N)
Sept. 23: Nerja
Sept. 24: Nerja to Ronda (2N)
Sept. 25: Ronda
Sept. 26: Ronda via Arcos to Seville (2N)
Sept. 27: Seville (drop off car)
Sept 28: Seville to Madrid (2N)
Sept 29: Madrid
Sept. 30: Depart Madrid