Your theory contains lot of nice details, but fails on other facts because you built the theory around a preset goal - which is to prove that Sasuke and Naruto will obtain similar power. In my opinion, the answer to all question is in Rikudo's decision to give his heritage or will to the younger son. From that, all conflict between Uchiha started, and everything started for the shinobi word. While many think Rikudo's action was a simple word, I doubt it was just mere words. So I made many interpretation.
Before I start my argument, I want to say that Hashirama and Madara were never the sort of Yin and Yang your are talking about. Hashirama without having any tailed beast was able to create things and maybe I can say create all things he wanted. Just check his fight with Madara and how he created these wooden Titan to fight for him. Check the dragon that he can make. These things are living things at the level of tailed beast. Hashirama was a master of Yin-Yang release.
Now:
1. Rikudo's power
I believe that Rikudo's power was contaminated by Juubi. That is his physical energy was contaminated by Juubi's physical energy and his spiritual energy was contaminated by Juubi's spiritual energy. Thus, The Senju inherited a strong body with life force but with some of Juubi's life force (Yang). The Uchiha inherited Rikudo's eyes with spiritual energy along with some Juubi's spiritual enrgy (Yin). With times, as Rikudo's DNA weakened along the genealogical tree, Juubi's power started t compete with Rikudo's power in both lineage (younger and elder son).
So, I believe that Sharingan was the manifestation of Juubi's spiritual energy, and Mokuton was the manifestation of Juubi's physical energy. The reasons is that each one of these was strongly inherited on the side of Rikudo that was compatible with it. Besides, Juubi's eyes on Madara's cave show 6 tomoes sharingan, and we have seen that Juubi's body is made of three.
I also believe that each of the lineage inherited a bit of the other side. But a key here is Hashimara's association with the Uzumaki. I believe that Hashimara is somehow half Uzumaki-half Senju. This is speculation, but we will eventually get an explanation.
2. The statement that Naruto only has Kyuubi's Yang is not true. Naruto has Kyuubi chakra and this chakra is made of Yin and Yang. These two represent the spiritual and physical energy. The Bijubomb is made of Yin-Yang in ratio 8:2. This is were Naruto and Sasuke differs. Besides, everyone is equating Uzumaki with Senju. While they are related, they are not the same. Thus Naruto is not actually a Yang opposite of an Uchiha. He is a totally different entity. This is why he is the hero of the manga just like Rikudo was the hero in the past. What I am saying is that we will see towards the end that Naruto is in fact the combination of Uchiha and Senju.
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