Its finally finished and in place in Babe Jr's bedroom.
I used 2 coats of primer and one coat of semi-gloss of trim paint to make sure none of the knots showed through. After the the first coat of primer I also used some paint-able caulk to fill cracks and disguise some of the nails. It took forever. I had the units propped up in my kitchen and could only work on one side at a time, then had to wait wait until it dried to flip it over to work on the other. But its finally done and I have my kitchen back!
We already had the bins on hand and they conveniently fit the cubbies perfectly. Only one of them actually has stuff in in right now because they were stacked together under Babe Jr's desk previously. I actually bought them several years ago to use for her Easter basket; they've served many storage purposes over the years. We have some reorganizing to do now. The cubbies on the wall side of the bed can be used to store things that won't be needed very often, like off season clothes. Both sides are finished and trimmed out the same way, so the bed could be placed in the center of a room with bins in all 6 cubbies.
I didn't trim out the section at the head of the bed like I did the foot due to the layout of Babe Jr's room. We're planning to do a headboard eventually, probably something upholstered. But if you trim that end you can center the bed lengthwise on the wall like a traditional day bed. This is really a versatile design, and even though it was time consuming for me since I could only work on it in spurts, it was fairly simple to construct. Here's the link again for plans. Ana White Daybed