I know what I would do in your position but its a bit tricky to describe but I'll try.
Get two pieces of wood, say 2" x 1" approx, 18" long each.
Drill a small hole about 2" from the end of each piece and put a nail or bolt through the holes so that you have in effect got the two pieces together that could measure an angle.
Into the other end of the wood, close to the end and facing each other put in a nail (the longer the better)(use round wire nails with a pan head It will not damage the roof.
You could then insert one of the pieces through the open light leaving the other end inside.
Close the two pieces up so that the nail on the piece of wood on the outside is on the roof of the van, close up the piece of wood on the inside of the van until the inside nail is resting of the ceiling of the van.
Here's the important bit. When you are satisfied that the two nails are both touching their respective surfaces using a pencil draw along one piece of wood using the other piece of wood as a rule. This will give you an angle
Now open up the pieces and in the comfort of the 'van close up the pieces again until the pencil line corresponds with its previous position.
At that point measure the gap between the nail surfaces and that is the thickness of your roof.
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Having given it a bit more thought I can only reinforce the bit about the 'longer the better' as far as the nails are concerned. This will allow you to overcome any lip in the existing skylight.
------------- How come when some people visit the fountain of knowledge, they only gargle!!!