Seems like a bit of a porcine overflight situation mate!
I cant really see the fuel molecules being polarised enough to cause a 'fuel molecule lineup'... especially not at the kind of speeds fuel's gonna be screaming through the lines at anything over idle.
Try dropping a magnet in a tank of petrol and see if anything sticks to it
Also I dont think 'ionizing' fuel would be a good idea, seeing as a real ionisation process tears a molecule into two separate charged parts. To do this you need two highly electrically charged plates anyways, magnets will not ionize anything if I remember correctly