I’m assuming you will visit the convent in Tomar as part of your time there. It is a definite ‘must see’. Your list in the area is a good one even though Nazare may be somewhat disappointing - it was to me. Be sure to go up the hill in Nazare, either by funicular or driving. This is my favorite part. But, lunch on the beach might be a good way to spend some time in the town.
Other seaside towns that might be of interest - São Martinho do Porto, Foz, Peniche. Ericeira is further away but might be my favorite.
Alcobaça and Batalha are both very much worth your time. It will likely take about two hours for each. But, I visited them both the same week and, frankly, have a hard time remembering the differences. I like the story behind Alcobaca better - it’s a love story...
Almoural castle is also worth a visit. If you can take a boat to the castle, it is a lovely way to approach it. Bear in mind it is a ruin. How much time you spend will depend on how much you want to explore. An hour is likely plenty of time.
You can easily see Obidos in a couple of hours. It’s very crowded with bus groups. If you don’t have time to see everything (which would really be pushing it), Obidos might be the place to drop due to the crowds.
For Coimbrã, Go Walks does great walking tours of the town including the university and library. It is a very reasonable walking tour. The food in Coimbrã is very good. The town seems to have a higher ratio of very good food than most towns of it’s size. Conimbriga ruins outside of Coimbrã are reportedly very nice, but I haven’t been - so can’t give a personal opinion. Two nights is likely about the right amount of time.
