I've used a cat litter freshener (a powder by Arm & Hammer) on smelly carpet and it should work for the trunk of a car. I'd sprinkle quite a bit of it and then leave the trunk open as long as you can and vac. it up after awhile but leave it as long as possible.
I don't know if this will help but I think I read somewhere that you can use fabric softner sheets to take musty smells out. Perhaps if you leave one or two of them tucked somewhere out of sight in the van, it may take away some of the smell. Good luck.
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