OK, I've downloaded your Mod and played about 150 turns on a fast speed at Prince level just to see what you have done.
Love what you've done, the Mod plays quite well.
However, my only criticism, and I experienced the same issue on the B5 Mod, is that you spend so much time building infrastructure, because there's so much of it, that there is little time to build ships. If you forgoe the infrastructure then your ship building will take even longer, leaving you largely defenceless when the pirates arrive.
The early game, say, the first 50 turns, you do have time to get some scouts, Colony ships and Planetary Defence ships built, but then you start getting bogged down with building the infrastructure you really need to be able to compete with the AI civs.
My suggestion, for what it's worth, either reduce the build cost of your added buildings by 50 or 60%, increase research times so you don't get loads of new buildings available to you every 10 turns or so,
Other than that, you've done some great work.