First, I made a few modifications to the rack to simplify the project. The V2 is unique in the way its rack bolts to the main frame where the front two of the four vertical stays bolt both to the top rack and the frame. On the V1 the stays are all welded to the top rack and bolt to the frame, and on the V3 everything is welded together. The bolt-on stays on the V2 stick out past the plane formed by the edge of the top rack and the welded rear stays, so if you strap a flat thing to the vertical rack (like a sheet of plywood, for instance) the front stays will mar and gouge the surface. I did a little more work with files to get them back to a position safe for cargo. I neglected to take before photos, but the notes on the Flickr pages should be clear enough to anyone who's spent time with a V2. I painted the filed surfaces with clear nail polish as a quick-and-dirty rust preventative.
This let me make simple boxes without any weird contortions to make up for the funny shape of the bike.
The boxes themselves are made from almost a whole 4'x8' sheet of 12mm marine plywood using glue-and-screw assembly with 3/4" quarter-round oak trim on the inside edges. The width of the vertical rack is 10" at it's base and 7" at the top rack. Each box is 13" wide at the base and 16" wide at the top, with the same 1.5" bottom-to-top slope on each side to match the rack on the inside and look nice and symmetric on the outside. The slopes on the front and back were chosen to be reminiscent of a Bakfiets and maintain heel clearance for the pilot. The finish is a water-based stain under a UV-absorbing spar varnish, both low-VOC.
The baby seat is a second-hand infant car seat with the carry handle cut off. It's strapped in with a high-strength NRS cargo strap with a layer of closed-cell foam (pipe insulation) between the seat and the box for suspension. The rain cover shown is the same UPPAbaby Bubble that Totcycle used for his Madsen infant seat. I'm less than impressed with the cover, as it doesn't actually act as a rain cover because the ventilation mesh on the sides isn't covered by the rain shield. Also, the rain cover is also the sun cover and therefore opaque. This bike needs to be all-conditions for Portland weather, which means great rain protection while letting Jasper look out and us look in. It'll do for now, but Katie and I are scheming a sweet ventilated rain cover for the whole box.
Also in the works is a matching top deck and dyno-powered lighting system.