Edit: this was in response to a post from Kahuna about a seed that changed between 6.000 and 6.001. I'm not sure where it went.
I don't know why 6.001 would have altered that (edit: yes I do: "The game no longer seeds wormhole guard posts on wormholes that lead to nebulae"), but if you want to run 6.000:
1) From your AIW install's RuntimeData directory, copy your Saves/ folder, settings.dat file, and inputbindings.dat file to some safe place.
2) Reinstall:
- If running steam, just do verify cache
- If running non-steam, just run the installers from here:
http://www.arcengames.com/w/index.php/aiwar-downloads; you could even just put it in a different place than your 6.001 install instead of deleting that one first.
3) Copy your Saves/ folder, settings.dat file, and inputbindings.dat file into the new install (in theory the steam verify-cache operation shouldn't eat your Saves folder, but it will eat those two .dat files).
4) Run that install, dominate galaxy as planned.
Let me know if you run into a problem.