Just bought an e-150 (standard roof), and am in the middle of this same decision. Considered Thule 300 gutter mount towers. Easy to find on CL or eBay but yes, the longer bars would be harder (read: pricier) to find. Current plan is to look for a used 3 bar ladder rack set. Still researching what brands are better, with the thought that cheaper ones might be more prone to rusting.
I am mostly hovering in the background until I learn the culture and board layout. Even though I have a standard roof for the time being and this is generally a pop-top forum, it looks like there will be a great depth of info on camper vanning in general.
Uploaded a pic of one of my Frankensteinian rack projects from a past vehicle..
http://www.sportsmobileforum.com/for...cture33604.jpg