It will not provide 9V. It is a 5V maximum processor.
Does it regulate these down 5V or 3.3V depending on which pin you connect to?
Those pins are, generally speaking, outputs. Don't try to shove stuff into them.
Will the VIN pin provide the full voltage of your power source?
The Vin pin is after the reverse polarity protection diode so it would provide what you plugged into the power jack, less about 0.7V.
If you are running from USB I wouldn't be using the Vin pin. I don't think it is supposed to be a source of power from that. I might be wrong.
I understand each pin provides 40 mA ...
That's the absolute maximum rating. I wouldn't design around that. Also there are limits for groups of pins.
This might help: