Woah, woah, woah!!!
3) Overlay of CB
That's your problem right there.
Never ***EVER*** overwrite your stock files with mods. (Only the imagepacks, since they are fully backwards compatible with savegames and PBW.)
You can add races to your stock se4\pictures\races folder no problem too, just don't overwrite stuff or put modded AI files into the stock folder. Modded AI files need to go in the se4\modname\pictures\races folders.
(Note: first, you'll probably want to restore your stock files from CD)
Here is how to install and play CB:
Step 1) Extract the zip to your SE4 folder (it will create a CB1.6 folder)
Step 2) Edit path.txt. Change the "path:=none" to "path:=CarrierBattlesV1.6"
Step 3) Run SE4.exe
These same steps apply to 99% of mods out there. Some have wacky directory structures in their zips, but all the major ones will work right.
To change mods, just change the path.txt, and run Se4.exe.
PS:
The mod launcher is overrated. Editing the path.txt yourself builds character