Is it safe for me to rename .esp files from mods? I have several mods that installed files with names that aren't even slightly like the mod name. It's a real pain when your trying to chase down a conflict or something is causing an error but your not sure what.

Technically, yes. Practically, no. You're going to make BOSS sad. You'll have to set their load order manually, that is.

Not really. Because of http://www.creationkit.com/GetFormFromFile_-_Game, which looks at the file name, any mod that references that ESP file name will break. I would only do this if you knew for a fact that no other mods reference them in scripts for compatibility reasons.