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case up a bit and the 1/2 molding will force it from the wall,
so that means the case is just not going to be straight
and stable. How best do I handle this?

I've always cut out a section, a curve or whatever at the back of the
bookcase to conform to the moulding. It's dead space anyway because your
bookcase is going to have at least a few inches height of toe kick, right?