Of course, most, if not all of the ambiguities could be explained by the writers getting sloppy. But that's NO FUN. So here we go.
According to Gai, Scrimil was created by Mina. Mina missed Gai and wanted him back. Because of her Creator Seed, her strong emotions were able to take on a life of their own. This new creature knew nothing except the desire to have Gai back, so it did whatever it could to fulfill that desire, including using the powers of its former "host". It gradually took Mina over, determined to use her Creator Seed for its purpose.
Mina likely had no idea what kind of power she had, or what kind of havoc it was wreaking. For most of the scenes between Mina and Scrimil, Mina doesn't even acknowledge his presence. Perhaps she didn't know he was there.
The series is pretty vague about how one becomes a Harmony God(dess). Perhaps anyone with a sufficiently large amount of Sohma can fill the role. Perhaps there's a special inborn Harmony God ability that one must have (I'm partial to this one).
If you take the first option, Scrimil had Harmony God powers because Mina's desire was strong enough that it imbued Scrimil with a fantastically large amount of Sohma.
On the other hand, one can assume that a Creator God can create pretty much whatever they want. If Mina's desire was for Gai's return, her Creator Seed might have created whatever type of creature would be able to fulfill that desire.
MIna created a new (but empty, as evidenced by his behavior in the first episode) body for him, and later separated Gai from Shulato and put him in the new body.
My guess is, the Creator Seed power is inborn. The problem is, the power must be balanced in order to work correctly. For some reason, Mina's power was activated by itself, without another seed to balance the force. The imbalance caused the power to go berserk.
Just a thought: Perhaps both Tenkuukai and Earth were supposed to have Creator Gods and Harmony Gods. If so, who was Mina's counterpart supposed to be? Yumiko, maybe?
Because Scrimil told her. As a Harmony God, Scrimil would have been able to see what happens in either world. If we assume that he was "born" soon after Gai first disappeared, it's possible he could have watched the whole story.
She didn't. Scrimil did. By the end of the series, Scrimil had completely possessed Mina. He thought that since he was a Harmony God, it was his duty.
Sohma color appears to be tied to a person's personality and character. As an artifical being, Scrimil wasn't really "good" or "evil", and therefore would not have had white or black Sohma. Red Sohma was something in-between.
Theory #1: Shulato somehow removed Gai's Creator Seed. That way, Shulato could become a Creator God once again, but Gai could stay on Earth with Mina.
Theory #2: Shulato calls it Gai, so perhaps it actually is Gai. Shulato's and Gai's Sohma merge again, but the "Gai" copy that Mina created remains behind.
Theory #3: It's Mina's Creator Seed. Shulato would need a second seed in order to become a Creator God, but he didn't want to leave Mina without her brother again. Furthermore, if left alone, Mina's seed could cause more havoc. If he takes Mina's seed instead of Gai's, Tenkuukai has their Creator God, Earth is safe from creatures like Scrimil, and Mina gets her wish to have Gai back. Of course, that leaves the possibility of Gai's seed going berserk...
Scrimil wasn't created by Mina, but was born with Harmony God powers by chance, like Lakshu (perhaps he was even human at some point). Scrimil said that a Harmony God's duty is to create a new universe, so he figured that was his duty. He tried to possess Mina in order to use her Creator Seed power. However, Mina's willpower and love for Gai were stronger than Scrimil anticipated, and she ended up possessing him instead (hence Scrimil being absorbed into Mina's shadow). When Scrimil told Mina about Tenkuukai, she realized that she could use his power to be reunited with Gai forever. Driven mad by the unbalanced Creator Seed, Mina could only think of Gai, and set out to destroy everything she percieved as coming between them. In her mind, the universe was conspiring to keep her and Gai apart, so she had to destroy it and create a new one where they could be together. The shadow that Shulato drove out of her wasn't Scrimil, but the unbalanced seed.
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