Other two questions: Do I need to clean bob's armory? And War cry?
I'm pretty sure you're not supposed to clean any of the FCOM stuff. Whether that includes component mods, or just the FCOM_ plugins, I don't know. I wouldn't clean it though, if it needed it, I'd imagine they'd have released patches (as was done for WarCry 1.09).
EDIT: I'm with Phitt on the issue of cleaning stuff - I've never done it for a mod I haven't edited/released. It's not the end of the world if your LO is not squeaky clean, although clearly clean is better. If you're having trouble cleaning or deciding what to clean, I'd say don't do anything, it's better than breaking something - after all, the onus should be on the author to supply clean files (obviously for old mods this can't always be the case).