I can only get scores to send with no mods what-so-ever activated. I figured at least CSInput would be ok with sending scores since *everybody* uses it. I tried using a clean install, no better results. Any ideas?

CSInput isn't ranked. You can't upload scores with it.

Is there anything ranked like it that lets you use both sides of a controller?

Not that I know of, although some charts will have CSInput included, meaning you can turn off CSInput and still have the effects of it, while also having your score ranked.