Let me share my experience with powering the 5V pin.
I have done this with a Arduino duemilnova and 3 megamoto shields powered by a 12V lead battery. I used a switching regulator and a capacity to get 5V.
All worked fine during test (no power on the power lines of the megamoto) but with power on the powerlines and motors running the Arduino died after a while (about 15 minutes).
Trying to connect my PC to the USB resulted in the com port being recognized but not being functional. With a 9V battery on the power connector the USB and Arduino worked.
A couple of days later the Arduino worked normally again.
I never really understood what the problem was.
It may be related to powerspikes on the gnd
it may be related to the megamoto (but I have had no issue at all I relate to the megamoto).
I'm sure it was not a coincidence because it happened to 3 different Arduino's. All the exact same scenario.
I switched to powering the Arduino via power plug and a 9v battery as a workaround but I still need a decent solution. As I have plenty of (power consuming) shields I do not want to put 12 V on the power plug.
The shields I have are 3 megamoto's 1 ethernet and 1 GPS shield (and I also power a RC receiver).
I am considering to "cut" the power to the shields and power the shields separate from the Arduino. I would however prefer to understand what was going on and have a nicer solution.
Can anyone make sense of these weird behaviors?