Sorry if this question doesn't make sense or is obvious, but would it be alright to submit a complete, free-to-play game? 

There are some extra endings that Kickstarter Backers had paid for, so I'm not sure if that could/would have to be included or not, if it's okay at all. 

Whether a game is free/paid now or in the past doesn't really matter. As for Kickstarter exclusives, I suppose that all depends on how much you feel it matters to have them included vs. have them as exclusive. Either way is fine.