I have been experiencing usb shutdowns recently. I first thought it was a complete system lock up, but I discovered that the OS and my scripts are still active. Without USB there is no network or keyboard, aka not very usable. The system does give a 'Disabling irq 32' when it goes offline. The pi forums indicate that usb is over amp'd, so I connected a powered usb hub to it for testing.

On a forward note, I built the external circuit on perf-board and it seems to be working well. I did drop the low battery cutoff functionality for this version as I will probably rework the power supply again.