Do your cloning on a new blank layer above the D&S layer.
Why is it a bad idea that it brings along the existing layer mask? Can't you just paint it more or less as needed?
Oh yeah, it's probably the 4GB of RAM
Well, that sucks, but you'll probably have to save jpeg versions of your PSD files in order to be able to place them.
No, not at all. That shouldn't make any difference.
Something is strange here. Why can I see a black shape in your layers panel thumbnail, but I can't actually see it on your image?
The best I can suggest is a brown Solid Color layer set to "Darker Color" blend mode, and painted on gently with a low-opacity brush.
But I'm not convinced it's necessary.