OK I have modded the game beyond alot of what you have done, I have modded to the point where it will build space elevator, shipyard,deepcore,and then factories around it, research and wealth.... then it will build adequate population and food. It will almost never build the higher order manufacturing hubs like fusion reactor or central mine. I instead changed the value of Space Elevator to 2 and +1 every level now I have the planets on par, which is pretty amazing.
I changed colony capital cap to 5 and fortified colony from population mod to 8, civilization capital is now changed to 12 (why wouldnt a civilization capital have more to start?) Giving this space to the ai allows it to build powerful colonies.
I changed the military academy to produce available legions when produced. this is necessary as the ai doesnt produce enough legions to invade. I used pop balance mod garrison features on fortified colonies and capitals but changed the amount of legions available to 1 and allowed it to produce 4 garrisons which makes the ai far more challenging.
I cant find the xml which controls civilization targets when at war, here is the only problem left I have with producing a truly competitive ai. When the civs are at war ai fleets will simply hover on planets...they do not go after shipyards or starbases, well starbases sometimes but not nearly enough. The ai fleets should prioritize shipyards in order to cripple manufacturing, I cant find the xml to adjust priority. Civ priorities should be shipyards, fleets, planets and starbases....I have had ai fleets simply go by all three and simply hover on my planets without crippling me. I have modded everything else to competitive but this last thing is the most important. If I can adjust the priorities of the ai to include all 3 it will be truly challenging.
The ai has trouble building good fleets, is there a fleet xml which can be constructed as such: an xml that breaksdown types of fleets construction by logistic points pairing that with the types of ships and and hulls available eg civilization has 20 logistics, can you make an xml which breaks down what should fill that 20 like 2 medium capital,6 tiny assault, 2 small escorts etc and this might be called an assault fleet and then there could be a different fleet labeled defense fleet and it could have a different break down. Also the ai never produces support vessels/ command vessels with a bunch of fleet supporting stuff. I am going to change the ship defs and this might do it. It could break it down by creating a rally point for every 5 shipyards where ships can converge for fleet construction.
also you destroyed the slave path, the slave camps are too weak to produce a viable civilization so I changed alot of the slave mill, pit stuff back to version 2.0 levels.
Just some thought, I am passionate about this game because it has the potential to be the best strategy game of all time.