the main challenge you are facing is Region Booleans in Rhino are sometimes not that fast 
after finding the mid-point of each intersection line, you need to trim out a region (rectangle?) to create the slits
working on the surfaces in Y direction (A)
find intersection lines (B), take their mid-point (C), find the plane centerd on that point along the surface (D) and align that plane in such a way its “private” X-axis looks up to the World’s Z axis
at that point you can build rectangles using those planes, keeping in mind that X is oriented up, so you want the rectangles to extend from 0 to negative x, and along those plane’s “private Y” direction you might want the rectangles to extend equally in both directions
after that you create a Region Difference between each section and just the rectangles laying on that sections (to speed it up, sort of…) and what you get is nice bottom slits
then you can do the very same exact thing on the section in the X direction, but this time the rectangles must be created in such a way they go up, toward World’s Z axis, and in “language” of the “private planes” it’s +X:
final result:
Waffle Structure_re.gh (27.6 KB)
if you want a different kind of suffering… do you remember when you did the offset in the earlier stages of the definition?
you could create another set of offsets that exists only to be used as cutters… imagine for sections in direction X you create a set of shorter ribs in direction Y that are as “tall” as half their final height, and for the region in Y direction you create a set of X sections on the opposite side and do the same
I don’t really understand what you mean with this:
something like this, where the slits are all on just one set of elements?
Waffle Structure_re_re.gh (20.7 KB)
how do you know where to clip the other set, if the slits are all on only one set of elements
