1) there are no border crossings. If you're driving along the border roads and don't pay attention to the signs, you may not know which country you're in.
2) Roads are very well marked, and getting lost is pretty difficult. Also, there aren't that many roads. I usually switch off my GPS for Spain/Portugal. Driving is a real pleasure.
3) You don't say what you have researched, but if you're on a road trip its almost a crime to miss:
In Portugal:
Monsaraz (across the lake you can see Mourao)
Estremoz
Elvas
Marvao
Monsanto
Sortelha
I also enjoyed
Castelo de Vide
Monchique
Cabo de Sao Vincente
In Spain:
Aracena
Jerez de los Caballeros
Zuheros
Montefrio
Cazorla
4) Parking in Seville and Granada is a major pain in the ass. I would make advance arrangements to make sure your hotel includes parking and reserves a spot for you. I have done this all times I've been there and never had any issues. Also, in Cordoba, there's a somewhat expensive hotel (by Spanish standards), I think it was called Maimonides, that has underground parking and its exactly 20 meters from the Mezquita, which is super convenient for that 8:30AM visit (the mosque is free in the morning and the atmosphere is superb with less people). You need to phone them when you get to Cordoba so they can open the old city gate for you (traffic is restricted there). Other than that there is parking in Passeo de la Victoria, both free and paid (cheap).
Also, I wouldn't drive around Lisbon at all its all rather compact, since I find that the hotels in Saldanha are better value than the old town ones I never have parking problems.
You will also meet "parking helpers" who "help" you park your car in a spot they have "reserved" for you. Give them 1-2 euros or risk having a scratched car.