I had a look at your save. No comments on religion or diplomacy since I can't tell the history easily from your current save.
I like your layout of cities, and your fundamentals are good, as you've improved your land well and executed the war well enough to take out Joao.
I think you're lacking in specialization. Around the renaissance, the Immortal bonuses start kicking in (actually every era they get faster) and you need to match it with exponential growth in your cities. That's tough to achieve unless you specialize them. When I look through your cities, you have a specialized HE city with generals, but that's it. And even that city is pretty far from the action. I made my war city the one to the west of Berlin, anticipating its proximity to Joao and Mansa later, and I didn't plant any towns there, going for farms (later watermills) and mines instead.
You also haven't built the National Epic. Typically, that will either go in a wonder-spammed capital (good idea with an industrious leader and what I did for this map) or it will go in a food-rich city running lots of specialists. Judging by your GP points you've only raised 4 or 5 GP so far. You should have a lot more, either settled under representation, used for bulbing techs, academies, or merchants on trade missions so you can keep your science slider at 100% longer, or a golden age (artist). You haven't made good use of them in your game. The two spies that you got you seemed to have settled - I would only settle them if I had pyramids. Otherwise, infiltrating is much better. You can get a few strong techs if you infiltrate a nearby city, with your state religion, etc. That's even better than a scientist who only gives one tech. Settling gives you spy points, but the AI will react to that quickly and up the espionage on you, so it's better to send a ton of spies to a city, let them get to 50%, then infiltrate and steal right away before they adjust their spending.
You have no super science or super wealth city. Your capital is making 40 BPT, with NO UNIVERSITY. If you have lots of cottages (as you do) you'll want the science slider up high to get science from every city, so you'll need a way to pay for that. Many choices here - if you can get your hands on a shrine, spread the religion, build bank/market/grocer/Wall St. in that city, settle merchants/artists/priests there, etc. That one city will cover financial costs to keep the slider high, where your BPT would be better. Much easier than that, on this map, was what I did. Dortmond and Essen have enough food to get a GP in the renaissance. As soon as I built them, I ran merchants only in both. Send those guys off on a trade mission for 2000 gold, on your own continent. Can also provide money for upgrading maces quickly. Of course you need to be in Caste to make this optimal, otherwise you have to wait to build a market or something.
You're running nationalism, without the Globe Theatre. The two have nice synergy. If you're not drafting, probably Bureaucracy is better. If you are, build the Globe so you can draft every turn (pop 6, draft, grow back to 6 next turn - a city only needs two food sources on normal to do this). You seem to be drafting, but minimally. A good idea is to switch to nationhood during a golden age (like the one from Taj), draft like crazy, switch back before it ends, declare war and run some culture until war ends/draft settles down. You can run at a financial loss here since you'll get loot from cities, provided you're winning the war.
EDIT: In your case, getting commerce from everywhere and not just the capital, Free Speech is probably the best civic to run.
You have way too many spy points in Joao. I spied on him and Mansa exclusively for the beginning, and when I declared on him, I used two stacks. One had siege, the other did not but only hit cities with waiting spies. Check out my screen shots, I only had about 10 trebs to go with the rifles. CRII rifles and spies are fine without siege. If you're not using the points, you should have put them elsewhere for stealing. By the time I capped Joao, I couldn't even see his power anymore I had used them all.
One last thing, power is misleading. I would have no problem declaring on Mansa with 0.7. He capitulates pretty quickly. Those artillery are hard to beat though, maybe too late.
In my game, I bribed Stalin to attack him in the early classical age so he never even challenged me for lib. Too busy building troops to fend him off, but he did get grenadiers before I attacked with rifles. No cannons though, and he won't attack your rifle stack if you give one of them pinch.
Z