Which model/motor do you recommend for an E350 build?

[DzlToy]

Common Rail 5.9 swap with a ZF-6 and Atlas/HERO. If you are going to build a bad *** van, you might as well go all the way.

Second choice would be LLY, ZF-6 and Atlas/HERO. Chevy motors have been going into Fords for years, why should this be any different?

 

[Pinnacle Campers]

I think the more important consideration than windows or no windows is, do you need more than two seats right away? If getting a cargo are you ok with no seats/interior wall paneling for a while? DIY build outs of vans tend to take a while... A passenger van has seats and a fitted out interior which is more than just windows.
At the same time a passenger 7.3 is a lot harder to find.