Sorry for the late response iam very busy.
Just take your time, I don't mind. I have many other things to do as well ;]
This is related to many factors and i know that SQL is much better to handle then XML.
Hm, from my experiences it is not just "much better", but for bigger project is A MUST. You have so much work with this mod because XML files simply hold you back
But i dont have the time to change that many files from XML into SQL.
The point is that you don't need to touch any of XML files at all to have almost all content converted to SQL. The game uses SQLite database, and loads all those information by itself. In short, all you need to do is to enable you mod, copy game's merged database file (core data + your mod's data), and with the tool like SQLite Manager (plugin for Firefox) you can browse through tables, delete, update, add data. You can export whole tables to SQL queries that are fully compatible with the game. You can export the data to CSV and process it in Excel, etc.
Many information are visible right away, so to control and manage everything for your mod, you don't even need to test things in game or inspect the logs that often.
As for XML files, well... these are mostly useless here - you only look at them to check whether everything has been properly imported to database, and if it so, then you may get rid of them for good
And this all is not just a theory, it really works, and makes a life of a modder much much easier - and you definitely deserve this Gilgamesch after so many years of hard work with maintaining this project
Just an example: it took me one day to combine 170+ different mods with wonders to one mod based on SQL, and fix all the issues or missing info. And additional three days were needed to process graphic, and other things.
Summary of this:
- downloaded content: folders > 1000, files > 2000, size on disk > 1.3 GB
- final merged mod: folders = 9, files = 289, size on disk: ~83 MB.
Nice, isn't it?

Well, without SQL I wouldn't even bother to do such a thing at all.
What really needs attention are the resources, this files should all be merged into one SQL file.
Then PM me them if you like. I can convert any XML you throw at me to SQL in no time* ;]
* well, almost ;]
The most important part, that needs to be done is a complete rework of the flavors, which also is the reason for some strange ai behaviors, but with more then 5000 entries this is a huge project.
I presume that it will be more handy for you to edit all those data in Excel? If so we may discuss how to convert it there and back again, if you like ;]
Nearly all flavors are already SQL files, only the ones from other mods/addons can be XML.
As I mentioned, it doesn't matter what files you have on disk. The game uses only the data from database - so if you open Civ5DebugDatabase.db file with SQLite MGR after the game processes the data from the mods you have enabled - then you can export all merged content to .sql file. Merged content means: original content + .sql files from your mod + data from other mods with xml files. And it is easy to delete original content, so this way you have "all that hard" work with all those merging done by the game itself ;]