You better be damn sure you're flushing out your solvent . Solvents reduce a lubricants ability to lubricate. But I don't know how well the solvent is actually removing deposits, just by filling and rotating gears a few times...
I wouldn't necessarily be hesitant to use ethanol. But, I think it might be wise to run a flush fill of gear oil for perhaps a few miles. And THEN go back with your final fill.