If you read the label I think you'll find your cleaner was only suitable for steel and cast iron and should specify not suitable for aluminium. I used to use an aluminium kitchenware spray cleaner which was fantastic (about 30 seconds to a minute was all that was needed) but it disappeared from the supermarket shelves a few years ago here in Australia. You're stuck with the stains now but that doesn't affect how the engine will run. You could try having it very lightly bead blasted.