The wood is looking good.
As for protecting the wood when hauling, I bought one of the thin 3/16" rubber bed liners for a standard 8' bed and cut it down to lay over the wood when hauling things.
Also I would not get too carried away with staining the wood, if the truck sits outside in the weather you will be sanding down and refinishing the wood in about 1.5 - 2 years.