Thanks to all of you that replied...
Maatkara - These are actually all the things that I'm basically just making up... I'm going by what tiny facts there are and just building a story that is meant to be intriguing.
Here are my answers:
Smenkhkare is the son of Nefertiti, but not Akhenaten (same with Tut) - this explains why neither are shown with the royal family in the many portraits of them all together...
I wanted Nefertiti as the mother to Tut... mostly just because she is the first main character, and in the story they have many of the same traits anyway
I have Nefertiti intitially getting sick with the plague... then Ay and Horemheb working together to poison her... there is lots of evidence that Akhenaten loved Nefertiti very very much and is very weak due to his illness, so I have them counting on it destroying Akhenaten and throwing suspicion off them (this is also before either of them know about Tut or Smenkhkare, so they would be much closer to the throne)
I do have Ay as the father of Nefertiti... they are a lot alike in traits except that... well Nefertiti had no initial desire for the throne and has a kind heart (Ay obviously doesn't)
Horemheb I have as just being Ay's wingman basically... he is loyal to the royal family, but Ay really just takes control of him, corrupts him mostly
As the ending of my book, Horemheb leads Tutankhamen out fairly far in the desert where Ay is waiting and they murder him (bash to the head turns out to be fatal)
That being the ending... I have nothing thought up for Horemheb's political views
Again, any ideas, suggestions or constructive criticism (or ANYTHING that cannot be true in the story) I'd love to hear!!