the yang half is sealed in naruto, the yin half is in the reaper, fighting minato for an eternity. There is no way of retrieving the yin half. Kishimoto still has some explaining to do about what yin and yang really mean in this context. Which might just be the next chapter.
You can't tell which half is which just by looking at one: They're continuous masses of chakra that each take an individual form of the kyubi: like Sora's, for example - that was a different kyubi, from the same chakra source. Comparing the two halves might be possible, since minato separated them the best that he could. Naruto's kyubi is practically complete, but it has no/little yin chakra and is probably much weaker than the original kyubi. (or the one that kushina had) He can control his half individually, without the other part even knowing. If naruto ever got the other one back (if), he might need to learn how to control that one too.. and separate its chakra from its will again, and put those two halves that are left in a cage.. and then they might also merge.
Madara's jubi, as a result, would be a weakened version of what he hopes to create.
Conclusion: A good half of a valuable biju was lost when minato threw it away for some mysterious reasons.
as for swallowing the scroll-toad, it seems the usual practice in the land of toads instead of "assimilating" it and learning its contents. he basically gained a power from eating the key, that of opening/closing the seal. you could tell that naruto, too, expected a different "learning" approach