Hey, that's why you're allowed to post: To ask questions when you don't understand something!
1. That's the size. Same size standard as the alkalines in your TV remote and the flashlight you keep by your bed. 2/3AA is a cell with the same diameter as a AA, but only 2/3 as long, for example. There's also an A cell, which is somewhat larger in diameter than a AA.
2. Volts and Amps have quite a complicated relationship. Multiplied together, they determine the total power available, Watts. Increase the Volts by adding a cell to the battery, or increase the prop load to draw more Amps, and you get more power to fly the plane.
Amps are what determine run time. Draw more Amps, get shorter flights. That's why batteries are rated in terms of milliAmp-hours, or mAh. Divide the capacity of the battery by your average Amps during the flight to get a rough idea of run time in hours. Don't forget to convert units, though.
One weird relationship is, when you increase Volts and don't change anything else, Amps also increase. That's why you'll often see people reducing the size of their props when increasing the voltage in their batteries. It's to keep the Amps the same to maintain the same run time, and/or keep the Amps below the maximum capacities of the motor, speed control and battery.
3. 3D is a "buzzword" that simply describes extreme, high-G aerobatics where the plane's wing is basically in a stalled state for extended periods of time. The plane remains in the air solely on the thrust of the propeller instead of the lift from the wings.
4. Oooh, you did your homework!
What you missed are losses. Charging isn't 100% efficient, and in fact is far from it. The extra hour is to make up for losses during the first three. It's overkill, and in the long run may do some slight damage to the battery. If you want, you can feel the pack periodically to see if it's getting warm. When the battery feels warm, it's charged and ready to go. Another option is to get yourself a peak detect charger with adjustable current. You can cut your charge time down to 30 minutes, and the charger automatically detects when the battery pack is full.