Ah..you know I did not even consider that you were playing as Joao, so Sampsa's idea on BW first makes sense in this case, and as I mentioned sometimes an alternate approach than the standard is recommended. Traits and starting techs can impact early decisions quite a bit. Regardless, it is still a good axiom to generally consider food first.
That plays a bit into the whole monument thing. In general, you want to avoid having to build Monuments or even teching Myst if possible, by making wise settling decisions. However, sometimes you have little choice when the seafood decides not to swim close to shore. Again, I will emphasize how FOOD is key to this game, so the simple answer to your question on the Monument for those seafood spots is that it is a faster way to get that food online.
In preparation for an HA war I often have built a chariot or two anyway waiting for the appropriate techs, as I have horses obviously. A couple don't hurt to have. One can become a good candidate for a Super Medic, and another maybe to catch the stray axeman should they exist. Maybe become a second medic or visi-scout. Plus, they are cheap.
Honestly, if you had horses up immediately, chariots would have likely been sufficient enough to at least take down HC earlier, although they were clearly not in a great position relative to sufficient food. Sometimes though I will just make the sacrifice on long term potential of a city just to get horses up asap, even settling on the resource itself.
Not looking at the map at present, and ideally you'd have settled a couple of more cities, but at this point you can focus directly on the war and gaining more cities that way for the time being. If I recall, you had quite a bit of jungle to the south - a lot of land really, so you can eventually settle that area based on relative resources. But focusing on joining the Incans to your glorious empire sounds like good short-term goal.
As for the scientists (specialists) your first goal is to get up a library, most likely in your capital, so that you can run scientists asap to produce your first GS. In many cases, you just create the Academy in your cap to boost short and long-term research based on the capital's likely cottage growth and Bureaucracy later. Lisbon is not a Bureau cap. If you have a good alternative (if I recall you had a coastal city SE of your cap with a lot of flood plains for cottages) you can create the Academy in that city and build the Palace there later. Another option is to bulb something like Mathematics, which while not technically an optimal thing in terms of beaker cost ROI, an early bulb of Maths does pay back in other ways like the boosted forest chops and trading it away for other techs like IW or Alpha, etc. I usually only do so if my leader is Philosophical, but I've done in cases where the immediate benefit of the Academy is not so great because of starting position like Lisbon (well, it does have the gold tile but otherwise not suited for cottage city). And on higher levels like Deity, that Maths bulb can sometimes really pay back sooner than later.
Other Libraries can go in commerce cities (cottages) but not every city necessarily needs one. High food cities are another good option to build a library since they can grow into the scientists, and you want to be able to run those scientists early in as many cities as feasibly possible relative to food and other resources.
800 BC is more than a reasonable date for an HA attack especially on prince. Just be cognizant of any metals HC might possess and look to rid him of it asap.
yes, IW is generally not something the Human will tech unless absolutely necessary. On high levels it is easy to trade for early. On low levels like Prince you may have to end up teching it yourself at some point depending on known AIs and their tech pace/willingness to trade, but it is still very much not a priority in most cases and you can usually hold out long enough just to trade for it.
With that said, I will mention a little bit about AI priority techs vs. optimal human tech pats. AIs are clearly coded to emphasize certain techs like Iron Working and, well, most military relevant techs (Feud, Construction, Machinery, Engineering). These are tech that if you have sufficient trade partners that you will always be able to eventually trade for them. Religious techs and Monarchy are often AI priorities too. So the point here is that the human techs around these items toward techs that are actually more beneficial to us anyway. AIs love Calendar as well.
tile rather than a 3
flood plain it could if it took that tile away from Oporto. Because its already size 5 and would go 
with 1 more population, the 1
1
.
which will give a Great Scientist in 17 turns (9 if Philosophical). It's ok if it it's a bit later due to whipping and repopulating or to help quickly get another unit out, but generally you want to rush the first Great Scientist so that it can start an academy in your capital city for +50%
. After the GS finishes, you can move it to your capital (or highest 
per city, granting +1
points on just one opponent (should do immediately or shortly after meeting the civs). Generally put them on the one you think you'll be trading with the most that game and is hopefully close to you. This is so that you are able to steal a tech or two later in the game with spies or to cause a city revolt when your army is ready to take the city (this makes all defenses go to 0% for the turn without catapults/trebuchets/etc.). If you're about to kill Huayna Capac, don't put it on him. If you want to focus on improving your own tech and empire for a long while, then I'd put 
enabled.
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