I cut tenons in the stretchers for the legs; these stretchers are flush with the outside faces of each leg for the purpose of workholding. The shoulder-to-shoulder measurements on each stretcher were taken from the distances between mortises in the benchtop.
All stretchers are finished, I will wait to completely set them till final assembly.
At this project's beginning, flattening the top by hand seemed quite daunting. Now I have flattened the top and underside several times (with each lamination), and grow more confident in the process. I have found that a scrub plane, something with a small reference surface, is good for removing lots of material across the grain. A big jointer plane (mine's a stanley #6 which some might find too small) with a large reference surface is good for flattening peaks and valleys on a bigger scale, and a smoothing plane (#4) is good for any cleanup of plane strokes. My #4 is a crappy Harbor Freight $12 plane that performs beautifully with a stone-sharpened (and strop-polished) iron, and a sole that require about 30 minutes of flattening on a tile with varying grits of sandpaper.