First make sure that the center/profile piece that runs fore-and-aft is not warped. If it is warped you'll have to get it bent back to flat status by slightly dampening each side and laying it on a flat surface with weights on it. You may have to 'counter warp' it a bit to get the flatness needed after the weights are removed. An alternative approach is to cut a new center piece from a sheet of flat stock. An uncorrected center piece warp will yield a hull with a hump on one side and a hollow on the opposite side.
Next, make sure that each of the bulkheads is symmetrical to the left and right of the center line. Carefully trace the outline of a bulkhead onto paper, being careful to accurately mark the location of the center line. Cut out the tracing, fold on the centerline and note any places where edges don't match up. Glue a strip of wood to the bulkhead to raise any low area to match the shape of the higher side. Do not sand down the high side. There will be plenty of opportunity to sand down high areas when the assembled bulkheads get faired.
Check the fit of each bulkhead onto the centerpiece. If it sits too high in relation to the top edge of the center piece then file out the slot until the top edge of the bulkhead is even with the top edge of the center piece. If it sits too low then add a piece of wood to the slot to raise the bulkhead until its top is even with the top of the center piece.
Use a slow setting glue when gluing bulkheads into place. You'll need time to check for alignment in three planes: No twist fore and aft so that one side of the bulkhead is forward of the center piece slot while the other side is aft of the slot; No leaning for and aft so that the top edge of the bulkhead is forward of the center piece slot while the bottom is aft of the slot or vice versa; and No tilting to port or starboard so that top edge of the bulkhead is higher on one side of the center piece while the other side is lower. Don't rush through the gluing work - install a couple of bulkheads and let the glue set before installing a couple of more. Hint: use a small square to check alignments, and check all of them again after making an adjustment because it is easy to get things out of alignment in one plane while adjusting one of the others. Small squares can be had by cutting 1-2 lengths from square stock that measures 1/2 inch on each side - buy it at a hobby shop. Finally, I've found it beneficial to work from the middle of the center piece toward each end when gluing bulkheads into place, gluing a foward bulkhead and an aft bulkhead during each work cycle. This approach affords ease of access for the gluing in of each bulkhead.
The following books go into detail on these steps with the aid of illustrations:
Back?