2 extra days in either Spain or Portugal - where to go?

Add the days to Madrid and visit as day trips from there, Segovia and Toledo.

Madrid will be hot, too, but I imagine cooler than Sevilla. Suki is right, Toledo and Segovia are wonderful. I happen to not be a huge Madrid fan in comparison to other cities in Spain. My recommendation would be to stay in Toledo, the two nights, it is nice to be there after day trippers leave and Toledo room rates would be less. I would use one of the 3 days you already have in Madrid to go to Segovia.

I wouldn't necessarily worry about the heat in Sevilla - Madrid will be sunny and hot too, at the top of Toledo it will be scorchio, and Barcelona may be nominally a bit cooler but possibly more uncomfortably humid.

However, I would worry that with only two days, it's not really worth fitting in Sevilla given how much of that time will be taken up with transport. Personally, I'd add the days to your existing destinations and, perhaps, add a day-trip (or spread out the touring and perhaps on some days decide on a long leisurely lunch and shady afternoon break, rather than "intense" sightseeing all day). For what it's worth, I think Barcelona has the most to see in the city, Madrid has the better day-trip options and Lisboa is the most pleasant. I'd do 5-4-4. From B, visit Girona, from M visit Toledo and Segovia and from L visit Sintra (which could be hot too at the top). Or add Porto?

I heartily agree that you should see Toledo and Segovia. I would also suggest seeing Granada and the Alhambra. While Seville was our favorite city in Spain, it’s a longer distance and will be very hot indeed. Madrid was my least favorite city in Spain so finding other places to visit is my suggestion.

Or spend two days in Porto after Lisbon.

Leave Seville for a later trip which encompasses Andalusia. Though I like Madrid, I was there for museums. If you prefer narrow streets, architecture and history, perhaps use the 3 days there for 2 day trips to Segovia and Toledo? I am inclined to suggest Porto as well, as it may be less likely that you return to Portugal (not based on anything more than visitable cities and size of country).

Our plan was to do a day trip from Lisbon and go to Sintra. And then do a day tour from Madrid to visit Segovia and Toledo. Giving us 2 full days in Madrid and 3 in Lisbon. Most of our traveling will be done in the evenings or overnight giving us the most of our time in each city.

Please do not try to combine Toledo and Segovia into a single day-trip. They are in completely opposite directions and each deserves a lot more time than you'll have on a combined day-trip. Some of us think Toledo is worth multiple nights.