What plans are you working to? Does the body plan show the transverse sections up to the top of the gunnel? If so then trace an outline from that. If the gunnel has a horizontal plate I've found it convenient to try and make as many of the stanchions the same, glue them in position then run the gunnel. Leaves a framework you can apply masking tape to, then trim back with a sharp knife and peel-off and transfer to the flat plate for the bulwark. You can always insert extra stanchions in-between and sand back carefully.
If they're not shown on the body plan a good estimate is to look at the plan, and the profile, so that gives you the transverse step-in for the angle. And the individual height respectively and you can draw each pair of stanchions /stiffeners from that.
Depends how exact you want to be. I try and make everything as easy as possible. Cereal packet cardboard as templates, bla bla, usual. It might sound more complicated than it is.
... I thought the cut-outs were often referred to as rat-holes but maybe not always (slightly different reason).
Have a look at the chap making the Smit tug for inspiration. Can't remember the location of the thread. Different prototype, same principle. He's doing. A very neat job. TID lines should be a bit easier to follow.