The Shinigami Seal ... explained in its entirety
I wrote out my theory here a while back.
I wanted to clarify my thought process, because looking back at that post, it didn't come out very clean.
The following explains everything involving Naruto and the Kyuubi. This includes how the shinigami jutsu works, and allows Naruto to use the Kyuubi's chakra.
1. "The soul of the ninja that uses the shinigami jutsu... will battle the soul of his opponent for all eternity inside of the Shinigami's stomach."
-- Given #1 --
2. Minato devised a means to split the Kyuubi's chakra into 2 parts by manipulating the shinigami jutsu, enabling Naruto to use only 1 of the Kyuubi's chakras. Sarutobi also manipulated the shinigami jutsu to seal 2.25 souls, along with his own.
3. It is IMPOSSIBLE for the Kyuubi (even with its chakra split) to be sealed somewhere other than the Shinigami's stomach. This eliminates the thought of the Sealing Scroll having part of the Kyuubi inside of it.
-- Given #1,2,3" --
4. Minato separated the Kyuubi into 2 halves. The, he sealed the Kyuubi inside of Naruto using 2 seals. Sarutobi created 2 shadow clones of himself to seal the souls of the First and Second Hokages. He used his real body to seal Orochimaru's arms. Sarutobi's shadow clones each has the Shinigami's seal of their stomachs before disappearing. When Sarutobi sealed Orochimaru's arms, his soul was sucked into the Shinigami's stomach, and is destined to battle the souls of the First and Second Hokages, along with the arms of Orochimaru ( lol).. for all eternity. What you have to remember, is that the shadow clones are only chakra. In theory, Sarutobi could have taken the souls of as many people, as the amount of shadow clones he could make with his own chakra, as long as his soul is that last to be consumed by the Shinigami.
-- Given #4 --
5. Minato must have used the method to separate the Kyuubi into 2 parts. Sarutobi mimicked Minato's technique, so we can assume a shadow clone would have been involved. In fact, this is the only logical way for 1 person, to use the shinigami jutsu to split the Kyuubi in half.
-- Given #5 --
6. We can now examine the Kyuubi inside of Naruto. The Kyuubi maintains its form, very similar in nature to the rasengan. It takes spiritual chakra, and physical chakra. This must apply to the Kyyubi as well. We can see half of the Kyuubi behind a gate within Naruto, this is the Kyuubi's "soul". The other half, "physical" chakra, makes up the Kyuubi's cloak. We are able to witness this relationship and understand through the progression of the Kyuubi cloak's tails. It also gives insight of how the shinigami seal works, when it separated the Kyuubi's 2 chakras. The Kyuubi "Spirit" behind the gate, obtains more more control and dominance over Naruto, as the number of tails increases. This manifested when the Kyuubi came close to successfully forcing Naruto to take the seal off the gate. Naruto almost appeared to be in a trance in that manga scene, and just obeyed the Kyuubi. That is until Minato saved him.
-- Given #4,5 --
7. Minato appeared in front of Naruto, and stopped him from fully releasing the Kyuubi. Then, Minato used the last of the chakra he had (in that form) to close the opened seal. Minato disappearing, after using his chakra, is unmistakeably similar to that of a shadow clone running out of chakra and simply vanishing. This in essence how I justify my theory on Minato using a shadow clone to seal part of the Kyuubi.
-- Given #1,7 --
8. If Minato and the Kyuubi are destined to battle for all eternity, why is it that Naruto can physically see the Kyuubi behind the giant gate, but NOT Minato? It is IMPOSSIBLE for Minato to just disappear due to "running out of chakra". Taking this a step further... it means that Naruto is "Seeing Inside the stomach of the Shinigami". We have seen the shadow clone of Minato, but where is the real Minato? Where does the battle for all eternity take place?
-- Give #8 --
9. I theorize that we have seen Minato all along. Without a physical body, Minato's soul can take the form/shape of anything he wants. If Minato is battling the Kyuubi for all eternity, we have to assume this is a figurative battle, if we are not witnessing it taking place behind that gate. In fact... I theorize that Minato... IS the gate. The Kyuubi is in a figurative battle with the gate holding him back. I know you are thinking "Minato said the he hoped he never had to see the Kyuubi again, so Minato can't be the gate otherwise he wouldn't have said this". Sorry, but you'd be forgetting how shadow clones work. The shadow clone of Minato was made during the sealing of the Kyuubi, and had been lying dormant until the 8-Tailed cloak appeared. Not until after it used all of its chakra to re-seal the "gateway"/seal, would the shadow clone disappear and reconnect with the real Minato.
-- Given #9 --
10. Last thing I want to reference is when Orochimaru attempted to summon the soul of Minato to battle Sarutobi. Sarutobi freaked out, and said that he had to stop Orochimaru from summoning Minato NO matter what! Why this urgency and concern? It is due to the fact that IF Orochimaru had succeeded... the Kyuubi would have also been released from Naruto. Minato must be what is holding back the Kyuubi from breaking loose. Vice versa ...if Naruto had pulled the seal off of the giant gate, the Kyuubi would have been released from the Shinigami's stomach. However, so would have Minato's soul, but without a body to return to. I will theorize that his soul would use his son as a vessel, and imbue Naruto with his abilities if that happened.... not predicting it will of course...
Well thats about it. Hopefully this version is a little more refined and clear to understand.