Funny, the only time my bike died and threw me into a little panic: was on the 5 near redding. Im my case, a wire from my PCIIIr, (the one that picks up the pulse signal), had rubbed and frayed till it lost connection. Bike went flat dead like yours. That's the limit of my knowledge when it comes to ignition failure like what you're talking about.
Any FI codes?
The FI code that I got, and SubSailor and Madbuyer, got me thru my ignition failure.
Do you have a power commander, and you've bypassed it to see what happens?