Yea, the switch from auto-complete to company mode was annoying to get done right, but was well worth it in terms of accuracy. It also provides function signatures which my old setup didn't. I also switched to using virtualenv mode as well.

I can probably try and dig up the relevant part of my config, but since I'm using prelude as a base now it mostly just works with only a few lines of tweaking in my personal.el -- mostly just virtualenv locations and enabling virtualenv mode with a hook.