I work quite a bit with aluminum (machinist) and it is very easy to mark up because its so soft. You would be surprised how often even deep looking scratches dont get far past the surface. I have fixed similar scratches on vacuum plates used to hold down parts. I get a fine lapping stone and wet both the stone and aluminum with some wd40 and LIGHTLY let the stone glide over the surface. You will feel where it catches all the high points and when they're gone the whole surface will feel identical and smooth under the stone as it glides with the oil. Wipe it all clean with a rag and inspect the area, if it all looks clean and feels smooth then you can leave it alone but if you want extra insurance you can go over the area lightly with some red scotch brite (and with fresh wd40) and wipe clean again. Ive done this on areas that are supposed to seal on the gasket of the vacuum plate and everything seals fine. I bet your motor wont notice once you have a gasket on it
