I am planning to go to Cuenca from Madrid by train. I've checked out the RENFE website. Train joourney @ 2 hrs 15 mins.
If you prefer a day trip, you should look at the earliest depaarture ?
The earliest should be @ 8.50 am, arrive in Cuenca 11.16am. If you miss this one, the next train would depart 12.23pm, arrive Cuenca 14.45pm.
I've check out various guidebooks. Cuenca ranks the highest for small town trips. Recommended for overnight stay though.