When Zoisite took the crystals fragments out of the hosts, did they actually transform into the Youma they used to be or or did the spirit of the Youma fuse with their present identities and cause them to be new Youma with the souls of their former selves?

Likewise, when Kunzite turned people into Youma was he changing them into new Youma or were they possessed by existing Youma that merged with them?

It might be splitting hairs, but the implications make a big difference.

I kinda like your first theory about Zoisite taking out the crystals. I think it gives them an added depth because if that were the case then that means the crystals that were to make up the silver crystal (which is healing magic) was the only thing keeping them good xD

I also like your first theory with the youma Kunzite used. Considering that Metalia was an evil entity that sought to turn the hearts of everyone to evil, it would make sense for Kunzite to use a little of that power to use the evil in everyone's hearts to turn them into Youma xD

I like to think that Kunzite was physically turning people into humans. I guess there is a possibility that he could be turning people into past yomas. 

As for the rainbow crystal yomas. I believe in the anime their souls were fuse with pieces of the silver crystal? (I really never understood why Queen Serenity did that where in the manga the Silver Crystal was inside of Usagi.) So I guess their souls move to human to human taking their energy to gain enough power to take a physical form once waken by the Dark Kingdom. I hope that makes sense? Or where they actually reborn as humans?

Now, that's an interesting thought...