Coimbra or Tomar for a 1/2 day visit?

We visited both in 2020. We toured a church and library in Coimbra, and all I can say is Wow, Wow, Wow! The library is spectacular and the church so beautiful. We also had a tour of the Convent of Christ, a huge castle/monastery, in Tomar. It was interesting to learn about the knights, how they lived, etc. I also loved the small town of Obidos as well as Fatima. There is so much to see near Lisbon--Sintra, Cascais, and Evora come to mind. If the weather is rainy in Porto, some of these might be worth a look.

“I get the impression that Tomar might be better suited for a 1/2 a day visit, and Coimbra is more suited for extended stay.” The following thread may give you more insight in what you are looking for. With a limited stay it’s just a matter of researching the areas that meets your preferences. We found RS Portugal guidebook, & this forum helpful in our planning. https://community.ricksteves.com/travel-forum/portugal/tomar-and-general-itinerary-feedback
Edited to add: Ditto what djk said! ;)

We were in Portugal for 3 weeks in August and had the luxury of visiting all the cities you are considering. Unless you are devout Roman Catholics, I’d skip Fatima. There’s nothing there but the churches and miracle site, unless the thought of Confession in five languages, no waiting, appeals to you. The basilica is nothing to write home about. Not much of a draw for the non-Catholic. Half a day in Coimbra would allow time for a quick university tour, but only with a guide or at least advance-purchase tickets, if they are available. In November, though, the students will be there and there might not be long lines. A half day in Tomar, again, would be enough for a brief visit, but such a short time doesn’t really do it justice. Unless you have a burning desire to see one of these sites, honestly I’d dump the car idea, take the train, and stick with Lisbon and Porto. There’s plenty there to do/see in both cities. Adding the driving, parking and walking time for any of your options, realistically, you’d have to plan a full day for one of them. I think that five days split between Lisbon and Porto would shortchange both of them.

I would definitely cancel the car rental, if it is not pre-paid, and take the train directly between Lisbon and Porto instead. In my opinion, you will need that 1/2 day of sightseeing (either in Lisbon or in Porto depending on how you split your nights). There are still plenty of €19.50 promo tickets for the Lisbon-Porto journey on the fast "Alfa Pendular" (AP) trains (3hrs): 2 of those will cost much less than gas+tolls from Lisbon to Porto, without even accounting for the cost of car rental.
The only place to purchase the tickets is www.cp.pt.
Trains leave from Lisboa Santa Apolônia, which is walkable from the Alfama and otherwise very close to the Baixa and Bairro Alto. They arrive at Porto Campanhã, from where I am 99% sure you can take the local trains to more central São Bento (right at the edge of the historical center) for free with you train ticket (or just book a ticket to São Bento, it will cost the same). Or there is a light rail system that will get you to places immediately north of the center (including Bolhão) in a few minutes, if that's closer to your accommodation.