You can fix this. It's a pain but it'll work. Assemble the uprights and the bottom box. Assuming you're using plywood or solid wood boards to finish it off, use the side boards to plumb everything up. Screw the side boards into the bottom frame, making sure it is in-line with the bottom edge of the frame. Clamp the legs to the side board, adjusting for plumb and 90 degree angles. Drill your pilot holes, screw it in and, viola! Your uprights should now be much less whacky, maybe even perfect. If your top frame is wonky, screwing it to the now corrected uprights should set it straight.