Nice B-24 Andrew
I must admit that I have never understood the use of bare metal foil for masking clear parts, the adhesive is designed not to let go! I do think that it will stick, much, better to bare plastic, so a coat of Future could be the key (wash, dry, then dip your clear parts in Future, get rid of the excess by touching the corner to a paper towel. Cover the parts while they dry). If there is still residue this can be removed with, if memory serves me right (and don't bank on this) WD40! If there is residue the scratches may be in that? so once removed the appearance of the scratches may be lessened. Even so, as already suggested, carefully brushing on Future will, at least, soften the appearance of them and probably camouflage some. In any event the scratches do not take anything away from the build, just treat it as part of the learning curve