1. Shirou does not "excel" at reinforcement. He's actually pretty awful at it.
No, he's not. It's the one thing he can actually do well.
True, when he starts off he's pretty crap, because he has no training, but he has the potential to be good at it (as shown by Archer).
2. Sakura got her genetic code rewritten by Zouken, so her "natural" hereditary eye color would be purple.
Nope, genetics does not work that way. Zouken re-wrote Sakura magically, but you can't make someone a genetic Matou. Biology just does not work like that. Plus, even if it did, it wouldn't affect her eggs in the same way, since they are produced before she is even
born.
3. Prana constructs don't develop free will.
Not "free will", it's more like an animal. Sakura's familiars have the ability to act independently to a large extent, I'm working on that basis.
4. "Likes: Riding Pegasus with Aunt Rider", you do know the G-force of that thing will murder him, right?
Not if she flies more carefully.
5. "Flow and Transfer" is not a hereditary Magical Attribute, it's a school of magecraft.
Erm, what I meant what the Tohsaka style of magecraft. Which is definitely hereditary.
4. "Likes: Riding Pegasus with Aunt Rider", you do know the G-force of that thing will murder him, right?
Rider can probably go slow so she doesn't kill the kid.
The winds from it's wing buffets even while it's chill can destroy a small building and tear a normal human to shreds.
She carries Rin and Sakura on it whilst they're unconscious, so she is clearly capable of doing so without killing them.