Do NOT put a cover on your bike while traveling !! It WILL rip your paint up from the wind flapping against the bike. I don't care how well you think you have it secured, it WILL rip the paint up. I'm not trying to scare you, but I've seen this several times as I often go to places like Daytona, Myrtle ect with my Harley and I've seen first hand what covers have done to some of the most beautiful paint jobs in the world. Sad ...
You are in a tuff spot, but one that I'm sure several of us wish we could be in. You have the ability, time, health, $$$$, and toys to be able to travel and see the good ole USA. Props to you !!
First of all, I'd scrap the whole van idea. Your bike MAY fit into it, but it'll be tight and I'm sure you'll scrape up the sides of the bike at least once loading it into the van. I suspect it'll be a REAL PITA, and thus I think you'll find yourself taking the van on trips with your harley still in the back of it.
Here's what I'd do ...
I'd get myself a small car like a Neon, and a Haulmark enclosed trailer that both the car and the Harley will fit into. That way both are protected, and both can easily be loaded and unloaded. Depending on the size of the car, you'll probably only need a trailer that's about 20' long. Figure on the bike being 8'.