Although I cross cut the shelf boards on the table saw, I had to cut them long because of some problems with my cross cut fence, and then true them up with my hand planes. Everything else was done with handtools, so I decided to post this here. It is confusing where to post when your projects are of a "blended" nature.
Here is a picture of the ledger boards that I installed for the pine shelf to sit on.
Most of pine boards are pretty straight forward, just fine tuning the length to just fit between the rails and chamfering the ends. The end boards are a little different as you have to cut out for the bench legs. I happened to have two pieces of scrap that were he same width, so I used one to establish the reference space and the other to mark my cutout distance. Then into the vise to hand cut it.
Here is the finished pictures. I had intended to nail the boards down, but since they are tongue and groove and fit so nice between the rails I am having second thoughts. I think for now I leave it as it, except for applying some finish.