haywoodphotomaccom Can tell you more about roof installations at least. He swapped his from a low one to a high one. He also mounted his battery under the van just behind the rear axle. Where he put his you might be able to keep your spare tire where it is. Check his posts and super great pictures for more detail.
wl1193 had two batteries installed into the back corners under the floor of his EB Ford. I kind of like that location but you can only do the right side if you have rear A/C.
On my 2008 V-10 van I have rear A/C so I did the diesel van battery boxes in the stock location on the right frame rail under the side doors.
If your van is a diesel you can put two additional ones on the drivers side rail the holes are already there you just need to buy or make some spacers to clear the e brake cable. If I ever think I need more power thats what I am going to do.
To move the tire to the back is kind of a big deal. The eight lug wheels and tires are so big and heavy they can't really be mounted on the door like they used to in the old days. You need something like this.
They both are quite nice but they are both $600 plus.
Do you have a battery size or requirements in mind yet? That may help you decide where to put it/them.
At any rate there are a lot of good ideas on here just do a search for what you need and go from there.