I tested your mod, it works fine. What do I want to do, is to ask you about some instructions.
I've began to make my own tech tree, something like this (it was pre-alpha):
The idea was to make promotions special and make ship parts as equipement, not promotions.
If you've ever played FFH2, you know that there's an option for a galley to recieve different promotions in port - it could have skeletal crew (-1 str, +1 cargo space), buccaneer crew (+1 str, -1 speed), or sailors crew (-1 str +1 mov).
The idea is the same - you develop nuclear missiles, that you can spend some gold in one of your systems by pressing the "missile weapons" button for ship squadron, and you recieve -1 str +1 missile for small ships, -2 str +2 missile for bigger etc. The idea is to have different hulls as special free promotions.
I.E.:
Tiny hull
The ships of this design are fast and agile, but they have a limited firepower and can't carry turrets.
+15% vs. missile
Also the idea of turrets(point defence), shield and armor is:
turrets vs missiles (and a small % against tiny hull class, as they come close to shoot)
shields vs plasma and lasers
armor vs general damage
Gravity weapons are somewhat nasty because there's no particular defence against them, but they come in play late (remember those cool wormholes from the MOO? We won't allow such an imba weapon, do we? But we can have some powerful gravity weaps. which do a lot of damage to large/huge hulls).
Now there's a question - do you want me to try to improve current leaderheads graphics (if you like mine in the post above) and add some technoogy buttons?
Also I can try to play with customizable weapons system, if you liked the idea. Some python is needed here, and it would take some time.
Also why don't accept some flavoured name for the mod? MOO2Civ is not too poetic =). Something like the "Orion sector" or another option would be nice.
Notice the "dawn of man" text on one of my previous screenshots - there's a brief history of orion sector races, where have they come from and how.