The plywood that butted up towards the shower got wet frequently and finally rotted away. The bulkhead is made of two layers of 3/4 inch plywood. Having two layers actually makes repairing this much easier. Instead of worrying about getting a perfect fit and junction on a butt margin, I can step the repairs and grant myself a lot of surface area to glue the repairs to.
Instead of repairing the problem with a future problem, I chose to use 3/4 inch closed cell foam core boards. These are unable to rot but offer incredible amounts of strength. Being the same size as the old plywood, they fit perfectly in place. All I need to do is cut back the rotten wood with the larger side of the hole facing me in the head. This means that the first piece is cut out the largest, larger than the second piece which lays deep to it.
With all the rotten wood removed and cut back to clean and solid margins, I simply glued the foam core into place and glassed it all together. The result is a repaired bulkhead that won’t rot again as the shower will remain there.