When using the spell Stone Shape, is there any restriction on the minimum size of any of the 3 sides of the cubic feet?
For example, with 20 cubic feet, could someone manipulate 50'x50'x1" of stone? What about less than 1" to expand the other dimensions even further using simple cuts or crude shapes?
My assumption is that when dimensions are given in some unit, that you don't gain anything by reducing the dimensions below that unit size. There are some definite examples of spells where this is so - silent image uses 10'x10'x10' cubes IIRC - but that exact wording isn't present in stone shape so it's more or less left open.
You can absolutely do that, right up until the GM says no. The only RAW that might prevent it, is stoneshape's inability to produce fine detail. If the GM thinks an inch, or a fraction of an inch constitutes fine detail, he can justifiably rule against it.
One limitation is that it only works on one piece of stone so you could only shape one stone in a manufactured wall, not a large volume of a wall composed of many stones.
This is also debatable, and ultimately up to the GM.
Casting invisibility on a bag makes the bag AND its contents invisible. Casting Make Whole on a ship repairs the whole ship, not just the single plank you touched.
There's plenty of precidence for allowing a section of wall to be affected.
I myself once took out a rival wizard's tower by removing a thin, diagonal slice out of it and letting gravity do the rest. Not all GMs will allow that kind of thing, I'm sure, but since I had ranks in knowledge: engineering, my GM was inclined to let it work. :D