Can somebody please identify what these transparent marks are

Personally I can't see any real problems, leaves will sometimes have funny marks or shapes for no apparent reason. No plant will ever have 100% perfect leaves, 100% of the time. Your plants look very healthy and I don't think you have anything to worry about. Also, filling your pots right up would have provided much more room for root growth, which leads to more plant growth and your plant will receive a lot more light by not being shaded by the "walls" of the pot and this would also negate the need to use foil to reflect light to the lower sections. Hope this helps,........ Organoman.