I attached a save to demonstrate a mess I've managed to create by 10th century. My research was over 200 beakers 500 years earlier.
I took a look and I have some suggestions to get things back on track. First of all you should be, if not in beuracracy because your empire is too big, atleast in vassalage, you are afterall in war.
Judaism keeps you friendly with the egyptians and incas but those are quite easy to befriend anyway, and they aren't your neighbours and you don't have that many jewish cities anyway. Instead I think you should switch into hinduism to get peace with portugal, get some tech trades with arabia, buddy up with the dominant hindy block and it's very likely that it will become the AP religion. As the biggest player you'll own the AP in no-time.
Mutal, as a buddhist shrine city, should stop pumping out missionaries and focus on building economic buildings. Market, grocery and bank. Other cities, especially low in production can pump out buddhist and hindu missionaries.
There is a spot with three potential gold mines (and two food sources you can steal from another city) that you should settle. You have room for expansion as you make about 100gpt with the slider at zero, and the gold mines will make the city pay for itself soon enough (immediately if you sell the gold to an AI).
You have a bunch of resources to sell for gold. Especially marble. Unless you plan on building a marble wonder anytime soon there is no reason why you shouln't make money on this. It might benefit your relations too.
I see no reason why you are researching gunpowder. Your military is already everything it needs to be for a long time into the future and musketeers won't really change that. And the Incas are soon to get engineering so I'd trade it to them for something. In fact I would probably trade for both paper and philosophy and gamble that I could get to lib before them. But that's me. Some more strategic tech trading and you'll be ahead in the tech race again.
Espionage. Get rid of every specialist spy. And don't place your spy points on everyone. Place it on one or a few strategic targets, like the incas that will have some techs you might steal eventually.