Hi Bill looking at your box and at the different trays, and knowing that my question may be out of place I wonder what will be or is the total weight of the box empty.
I know you've built it sturdy and to last, I know that pine is a rather light wood but judging from the pics ( and that may be misleading) the whole box will be rather heavy on its own, and although you mentioned that you won't be moving it around much I think that being this one a prototype maybe on your next one you'd like to make it lighter so that you can include some more tools in it.
Maybe it is just my perception and I'm completely wrong.
One more thing; there is another way of making a small tray fitting on top of another one without using ledger boards that take up some room on the lower tray. If you make the top tray the same length of the big one and its bottom thicker so that it protudes about 1/3 of an inch you would get the same nesting effect ( provided that the bottom is fixed inside the sides).
Two strips of wood glued on the bottom would do the same effect, but I know the perfectionist that is in you so please disregard this last one.
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I also dream of a shop with north light where my hands can be busy, my soul rest and my mind wander...