Took a look.
Well, there's "transition" to late game or whatever, but that still doesn't preclude the fact that there were a lot of mistakes made in the earlier game, which is where most problems lie anyway.
It's hard to tell from late game saves what all has a occurred in the from the start, but I can glean some info from the save.
I'd chalked this up to several things - lack of focus, useless building, poor worker management, Great People or lack thereof and usage, poor tech decision, poor economic base, etc.
Nople is not exactly an ideal Bureau cap and has poor food, although FPs can be farmed. But you have made it your Bureau cap and murderized it in the meantime. One of the keys to the game, especially a longer term game, is to setup a good research and economic base. Much of this lies with the capital. Now, granted, very early the cap will take some hits with whipping to get out settler/workers for early expansion, but this must gradually, and as quickly as possible, transition to secondary cities, allowing the capital to grow or a) running those first scientists for academy and then cottage working. If a cap is not suitable for Bureau then it is advisable to look for a better spot. The fact that Nople has been whipped to the beejeezus is a glaring problem here..you have no reasearch base here, and Nople not great in the first place. Improvements around Nople are a bit hodgepodge.
Regardlesss, when I see stone right there my first though always is Pyramids. In that case, I'd be making Mids a priority in which case Nople can just be farmed and run specialists when it can, using Caste Systems at times. Take advantage of your great Spiritual trait. (Stone also allows one to use wonder for failed gold as well) Anyway, Representation is such a powerful early civic to have. You can still setup a bureau cap elsewhere if found, or otherwise set up some cites for cottages just to have that economic base, but with Rep get specialists, especially scientists or merchants running early is a huge boost.
Next, I'm don't think you have a plan or much of an idea about what to do with buildings. I see so many useless buildings being built. Granaries and Forges are the only must buildings, and when your Empire starts to get as large then Courthouses in some cities are needed. Obviously, you are having Strike problems now.
But speaking of Strikes, may gawd! why are you not trading resources. Trade resources for those you need as soon as you are able, and after Currency (such an important tech), trade what you can for any gold per turn. Renegotiate those trades as soon as you can for more GPT. I went in and made all the trades I could and put you in the black immediately. Plus, beg for gold from all Pleased AIs. Trading also helps boost diplo relations. Also, you are running Theocracy but not in a religion. That is doing nothing or you but increasing your maintenance.
Not sure keeping Monty as a vassal was of much use. He has nothing. I usually want my vassals to be able to do something for me like fight or tech, unless toward the end stages where I'm just looking to finish up the game. I would have put him out of his misery. Willem can do something although he does not have much at the moment. (Note: you can direct vassals tech path)
I'm not a fan of Knights or Catas for that matter, although Catas are not bad. However, Knights effectiveness is limited to useless on higher levels. But the big problem is Knights put you on a problematic tech path of techs AIs prioritize which a) limits your trading opportunities and b) takes focus away from stronger/better tech paths like Edu>Lib>Military Tradition for the much better Curs.
So at the core here, you've not setup a strong economic base really and likely teched a great deal of bad techs that you could have easily trade for. Furthermore, while you seemed very focused on getting to Catas and using them, there is a lot less focus on other important things and you put yourself in a position right now where you are very limited. Conversely, you might have gone for a better path to Curs, which are a longer lasting and more effective unit, bulbed your way to Lib>MT, back traded for all those techs anyway and generally be in a stronger position now.
As for this game, it may be salvageable. Catas are most certainly spent, so all I can suggest is sit back for a while and recover your economy while focusing on empire management to improve your cities and economy. Use that prophet for a golden age and spit out some great people like GSs and GMs to bulb some techs like Edu and use GMs for trade missions to the Temple of Artemis city. Look for good tech trade ops (including gold). Whip out some courthouse where you can and maybe build wealth in cities that just don't need anything. Some good cities could use some Libraries. Getting six Unis and Oxford up quick may help with research too but not a really strong Ox city has been established - still anything would help here.
It would take some time to get in any military advantage situation here, but you can still go for Cavs or a Rifle/Cannon/Artie combo and surprise some of the generally weaker AIs like Pacal or Capac.
Again though, much of your problems here occurred thousands of yours ago, so you may want to rethink some of your gameplay in the early stages.