@OP
Well, I opened your save file and had a look at it. I must admit, I did not play any turns. But I managed to see quite a lot.
On the positive side, your workers don't seem to be automated, and that's already a big plus. I'm quite serious here.
However, the rest is not so good. In the city screens you have everything on Default focus, Manual specialist control boxes not locked. On higher difficulties you want to have more control here. You had Marble, a lux resource worth 4 happiness, in the third ring of your capital Paris, yet you let Kiev - a city state! - to reach and take it, although it was FOUR(4!) tiles away from Kiev. As a result you have no Marble now. A bit too generous on your part, I'd say. Yes, you have 16 happiness, 3 cities and 1 settler on route I don't know where to (well, maybe for that 2nd citrus and bananas), but still. You don't want to let city states steal your luxuries in such a way. Your second expo Orleans had 9(!) iron in its 3rd ring and yet you let Sofia to have it, although it was also in Sofia's 3rd ring. I believe with a little effort you could have had it, seeing that it is the only iron source in the vicinity of your empire.
Let's recap the time: it is t164, 1040 AD.
You haven't yet researched Optics, now worth 2 turns of research, which would let you to embark and cross that little bay and destroy that barb camp near the Vatican City that both Vatican (faith) and Kiev (culture) have missions for. Both of them plus Wellington (food) in their vicinity have also issued missions for a trade route. You have 3 trade routes available, yet you're using only two land caravans. They are going from Paris to Sofia and Mongolian city Turfan. As your only coastal city is Paris, and with so much happiness to spare, you might have wanted to help grow Paris and send those caravans as food caravans from Orleans and Lyons to Paris, that would have resulted in more science generated in Paris than the current meagre +2 beakers from the route to Turfan. Alternatively, if you deleted one land caravan (or reached Compass for another trade route) and had two trading ships going from Paris to Kiev and Vatican, plus a land caravan to Wellington which cannot yet be reached by sea, you'd fulfil their quests for lots of influence. If you managed to destroy that camp, you had two allies more. If you're neglecting city states in such a manner, no wonder somebody picks them up, you don't even need Alex.
By the way, why do you have your army concentrated on the other side of your empire, far far from that notorious camp, and on the border with Theodora? She seems pretty friendly and inoffensive and a useful trading partner. You should be more worried about checking Genghis.
Paris is generating the most of your gold, yet you are missing a market there. You have picked and completed Tradition, yet your total income is only +20 gold? I'd thought you went Liberty if I did not check.
You picked Aesthetics as your second social policy, so I guess you're aiming for the culture victory. Yet your faith generation is exactly 0, although you have the Byzantine Eastern Orthodoxy which in your case would let you buy for faith Cathedrals(!), Monasteries(!!) and... Mosques(!!!). The exclamation marks are here for the degree of their awesomeness, yet you're completely ignoring them!
Your spy is in Mongolia which has 1 tech less than you and has a stealing chance in 32 turns? A bit too long a shot. Have you tried notIstanbul?
I'm pretty sure this game is still very, very much winnable at this point.
Just continue to improve your playstyle. Read a bit War academy articles, if you're into reading, alternatively you might want to check a couple of the latest SBFMadDjinn's youtube videos - Indian Culture victory and Poland liberty games. On Deity
. They are pretty old now and pre-latest patch but still valid, imho. Have less stress and more fun!