It said the rest went toward production of the xkcd book. I don't know if that means solely inventory and production costs, or if it includes administrative overhead as well (I would assume some)
Book production (cost of printing, binding, shipping to xkcd fulfillment center) - by far the most expensive thing Contracted design work ISBN registration A few FEDEX shipments for prototypes
[Ultimately, we agreed with xkcd to share the costs and deduct those from the total revenue before splitting the profits, but I needed to put a hefty downpayment and it helped to have the $ in the bank.]