I have a similar problem... 2000 Rodeo V6... When fuel level gets low the check engine light does come on. Thing is, you could have 1/2 a tank, turn a corner, and the fuel guage then shows "E" and the check engine light comes on. The fuel guage isn't consistent at all once it goes below 1/2 tank. If you park in idle for a while (really, it takes a few minutes) the fuel guage does rise again... I do know the "check engine" light relates to air getting into the fuel line (ie. the gas cap being left off). Could this problem be a fuel filter, fuel injector, or what???
Assistance is appreciated.