On the other hand, I should take down Joao NOW when he's weak, before he gets Longbowmen. No, Longbowmen aren't invincible, but they are a pain and it's always nice to avoid them.
I wouldn't worry about Joao getting Longbows any time soon - looking at the tech screen, he's much further from Feudalism than we are from Construction.
More worrying is our power graph relative to both of our neighbours. We are a prime target. And, though it seems they would be less useful against Joao, I would prioritise a few axes in case Caesar decides to try his luck. We can leave some behind, ideally with a couple of cats for company, when we launch our southern offensive.
There are concerns about the economy as well, especially what a lot of expansion will do to it.
I wouldn't be too worried here either, unless we plan on settling multiple northern cities and absorbing Joao's whole empire before we get Currency & CoL. If we settle only the blue site, and keep only two of Joao's cities, then we should be able to keep the economy afloat while researching the crucial techs. The gold and gems, Barcelona's cottages, and the spoils of war, ought to see us through.
And then there's the quest to worry about.
I think you'll just have to ignore that for the time being. Horseback Riding is a diversion too far at this point, and we won't be wanting to build stables until the more vital economic builds are in place. If and when we do go for it, the food bonus would be far superior to the HAs (unless we find ourselves in trouble at the very moment the quest is completed, of course).
Blue city, then, would buy me some time to build the other cities at my leisure. Which means I could then have time to devote towards units that could take down Joao.
I may be misunderstanding you, but it sounds like you're not giving enough priority to military builds
now. A DoW from Caesar could end this game very quickly. We need axes.
I'll send a Chariot into his territory quickly to verify he has no metal, then close borders again.
Definitely the right move. It would also be very useful to know his present troops numbers/types, and whether his capital is on a hill. The first objective of our campaign should be to take Lisbon and Coimbra (simultaneously if possible), so anything that helps us to estimate the number of troops needed to bring down the capital will be a real bonus.
I see no need to rush to war in this case. We should make sure we have the forces needed to swiftly eliminate Joao (or at least to cripple him), so as to minimise the chance of war on two fronts.
Oh, and bear in mind that razed cities can spawn partisans, but these disappear if the civ in question is eliminated (iirc - is that right?). A good reason to take the cities you want to keep
before razing the ones you don't want.