First of all, I read another post on here that someones fuel warning light quit working because ethanol melted the float. That would seem to be the most likely cause. I have seen firsthand the damage ethanol can do. I wish RE had put a trip odometer on the bike instead of the low fuel light. I grew up using the odometer, and on all the bikes I've had with fuel gauges, they always closely matched the odometer.
Second, since you actually ran out of gas, does your fuel pump still work ok? The manual seems to make a big deal about that, or maybe it's me making the big deal out of it, because I never heard of running out of gas destroying a fuel pump. I have been refilling my tank every 100 miles, to prevent the the fuel pump from destroying itself. Considering how fragile most modern technology is, I really don't doubt it could happen.