Don't sweat it, you'll get it working!
When using the old GC writer, be extra careful in naming files and what you copy and paste when doing things. I use the CG Data folder directly with a backup in a folder called "Previous Data_1." Make sure no duplicate files exist in the folder under different names. I have had the same starbase module problem as you! It was a pain to fix! To fix:
1. Get your file in the GC Data folder.
2. Run GC Write against each category (improvements, etc. Check every detail! And write down IDs to track them to be sure they are ok! At one point my IDs were so messed up due to GC Writer trying to fix duplicates, I had to loose my some of mod work and restore earlier work.
Get just the base data files working (no mods). And run the game and be sure your starbase is working (make it low cost so that you don't need to test long). Next, add in your mod tech files one at a time and run GC on each, checking them as it goes. Test the results to see if the starbase is still ok (should have no effect).
Add improvements one group or file at a time. And run GC Writer likewise as before (with tech files present). Test the starbase. And be sure you are not being allowed to build lots of improvements without having to invent the tech. If that happens, you need to go back to each improvement and set the tech_requirement field to the tech needed for activation (name or number, as needed). GC Writer loves to erase the tech requirement numbers and/or noun names when it gets confused about what tech does what when IDs are messed up as duplicate Tech numbers or duplicate requirement IDs in improvement files. If a data file is ok, be sure to make a minor change in order to make it write the whole thing to file; refresh, and be sure it didn't mess any thing up. And never try to work improvement file by themselves without the associate tech files also present in the folder. I did that once! Woops!
Once done, add your mod ship data files and check them.
Hopefully this will get you straight and the starbase modules working again. Check thier IDs also are ok and correctly associate to correct technologies requirement IDs; that is where the problem was in my case, if I recall properly.
Remember this too (from another thread at this site):
IDs:
a) The range of possible IDs for Wonders is 1-149.

The range of possible IDs for Achievements is 1-253.
c) The range of possible IDs for Trade Goods is 1-49.
See here for my set of combined mods from this site plus a few of my own (play tested and play balanced, howbeit to my own tastes - I play Altarian Phophesy version, but these should work in CG as well):
http://users.rcn.com/aulonacara/Galatic%20Civ/