The cushions are 2" fairly dense foam purchased from a local foam shop, cut to fit exactly. We found some cool patterned fabric, and with some basic fiberboard from Home Depot cut to the same dimensions, we stapled the fabric underneath.
The cubbies now have some simple baskets in them for storage, mostly used for drawing and craft material for our kids.
Total cost was roughly $350. The Trofast units were about $90 each, the foam was $120, the fabric was only around $20, plus we bought high quality paint from Benjamin Moore and few other incidentals.
Step 1: Get the Trofast units from your local Ikea.
Initially we thought about using a few of the units that already sit flat for wall or floor storage, like these:
but when we went to Ikea and took some measurements, we ended up with two of these instead:
My guess is that any of these would work out, though you may not be able to mix and match if the heights and depths don't align.