Does AP scale into your basic attack?

Against towers and inhibitors, yes.

There used to be a mastery that would take 5% of your AP and add it to damage to all targets, but it is no longer around.

Only on structures.

If your total AP is higher then AD, its based off that for structure damage.

Nope, which is why it doesn't make much sense that AP is becoming harder to buy, and AD tends to scale just as well. Autoattacks + abilities > abilities.