Hi,

Can you post the circuit diagram so we can see what's connected to what?

If you have an input with a pullup resistor (internal or external) and that input is pulled low by whatever is interfaced to it then current WILL flow thru pullup resistor and contribute to the total current drawn by the circuit.
Going to external pullup resistors powered thru a MOSFET won't gain much compared to simply disabling the internal pullups - as far as I can see.

The dropout voltage of the regulator doesn't have much to do with this. It's the "idle current" you're interested in, how much the regulator itself consumes in order to operate. The datasheet states 150uA max

/Henrik.