Install the remainder of the upper cabinets with the spacer box as an aid. Level the cabinets, screw the adjoining stiles to each other, and anchor the cabinets to the wall. The bottoms of the cabinets or stiles must be even on all the cabinets. Reduced height cabinets should be the same height at the top. Install the drawers and check the operation.
Drawers can sometimes go out of alignment if the base cabinet was twisted during installation.
Adjust if necessary. Install the adjustable cabinet shelves and verify the alignment. The shelves should rest on all four shelf pins. Shelf pins can be thrown out of alignment if the cabinet has been racked or twisted during installation. If severely twisted the cabinet may have to be loosened from the wall and aligned.