For my first attempt I did something similar to what you describe, starting with plywood. Then I had the bright idea to switch to posterboard for the template and it worked much better. I used next-largest and next-smallest stations to create a half-template that was the size of the larger station, but had a pencil line showing the edge of the smaller station for reference. It was then pretty simple to hold that up against the hull and determine where I needed to trim to get a perfect fit. I then traced back onto plywood, flipping the half-template to give me a symmetrical bulkhead panel.

I'm installing the bulkheads into the hull prior to attaching the deck (Etienne's method) for a few reasons, including that I know my hull and deck are slightly wonky, so by ensuring that the bulkheads are shaped correctly and symmetrically, it's helping me adjust the hull and deck to match how they should be.