I did a run with Roo that has a Game Over and the Bad Ending for Factory. Is that considered a failed run, or is it still a completion?

By game over you mean you used a continue? If so I believe that is still a valid run, as long as it was done in a single sitting and you did not reset or restart the game/console.

Yeah, I used a continue. That's what I meant lol. The run is done from start to finish, but wasn't sure if the bad ending for Factory is considered a completion.

If you are using continues and/or get the factory's bad ending, the run is still legal.

Awesome. Thank you for clarifying!