1. Your mods' loading order should be (for vanilla esms):
Fallout3.esm
Anchorage.esm
ThePitt.esm
BrokenSteel.esm
PointLookout.esm
Zeta.esm.
Unofficial Fallout 3 Patch.esm
...your_mods
CivisRomanus Unofficial Fallout 3 Fixes.esp
CivisRomanus Unofficial Fallout 3 Fixes Dialogues.esp
CivisRomanus Unofficial Fallout 3 Fixes Optional.esp (if you use it)
CivisRomanus Unofficial Fallout 3 Fixes Cheat Items (if you use it)
Use LOOT to set the main esms in the correct order. As you probably know, LOOT will *not* (correctly) sort *all* your 10000 installed mods.
Use the editor to manually change the mods loading order.
2. Clean up the main DLCs esms with the editor. *Do not* clean Fallout3.esm.
Check youtube if you don't know how to do this. There is a nice tutorial for Skyrim (as far as I remember, I'll let you do the honors) which *nicely*apply to Fallout 3 and New Vegas too.
I cannot say if it applies to Oblivion because I did not try that (yet).
3. Clean up Unofficial Fallout 3 Patch - see the article.
4. There is no real need to clean up the Fixes (all of them). I already did that.
5. As I probably specified, I do *not* use FWE/FOOK/WMK/MMM or whatever Batrachian/EMO/Vulpine/Vampiric/Ancient Elven/Ghoul/Happy Tonsures Cool Faces mods.
Please, don't ask about conflicts (if you are using them!) because you will *surely* have with both UF3P *and* the Fixes installed.

Happy Fallout 3 gaming.