Dave,
I've seen your/this project before, somewhere else. I was going to do a E-series onto an F-series using a 78 F-250 & mid 80's E-200 Van, but "Henry" made an Excursion so I quit the concept & moved on to other more unique ventures. . . 
BUT, in doing Research & Planning for the proposed "project" I came up with the concept below out of the need for both structural integrity & eye appeal.
It seems to me in your case you may want to consider running the Aero roof panel all the way across your F-100 Cab to it's windshield header beam or at least close as possible to that connection point as you can. I believe stepped the connections,
a "Z" or inverted "L's" in seam/ splice line of both body component assemblies will give you greater structural integrity than a straight butt to butt -- connection.
I know realize I say is lots more work, but it's mostly concealed on completion and will enhance your "Over All" quality & structural integrity of the finish project, don't you agree? I mean ladder frames work & flex, and uni or mono**** bodies do not, so we are talking about different flexion rates. Shear & twist will still occur so the monolith has to either be capable or tolerating flexation or surrender to it through failure. Flexation in sheet metal structure can result in "catastrophic failures", at least in engineering terms it's catastrophic. Cracks fatiguing loss of integrity, etc.
In aesthetic terms such a design change would also eliminate the "hoop dee doo" effect where Aero roof meets F-100 cab back, thereby giving you a single plane, roofline transition. Plus, it's a alot easier to "nail" single layer of a roof panel sheet to a compound laminate header beam stamping, than stitching two sheets together in a seam or butt weld, at least for me it's easier. It's easier to fine finish too.
In addition there is a beam formed around cab door you can connect/ tie Aero roof beam to at it's front "C" pillar of your sliding door. There's a roof beam on otherside
of the Aero roof panel and "C" piller behind driver's door of the Aero body too. Tying all those beams together will provide ridgidity & strength you'll lose when you cut both bodies to make that all important splice. The photo shopped image shows divergent planes. What I'm suggesting is a convergent single plane.
If you run into problems at compound curve where transition radii (radiuses) start I suggest you visit Ron Covell's video, or someone else's on "You Tube" on using an English Wheel. Just go to You Tube & search " English Wheel" you will find you have your pick of several different videos. They will teach you in an avaning what I spent weeks learning before there was a YOU TUBE. . . 
. . . .
I recently bought an English Wheel from Harbor Frieght for under $300 with a complete set of extra die anvils of different radii (radiuses). I don't use one a lot so there is no sense of me spending $1,000's on one. But Hey, for $300 it's well worth
it to me. The quality is good enough for occasional use. I'm not a production shop.
When you do this "One Off" or as you call it "Darkside Project" you may get people after you to do other such projects. I did but I do not want to go there again. I want to do what I do for the Hell of doing it, not for the money and pressure it brings. . . . Call it Old Age or whatever, It's not happening any more. 
Back In The Day when I was cogitating the F-250 + E-200 "wedding" it would have been a 460 powered 7 passenger that would have flown in the face of all Blowtie Suburbans. The key in that project was to start with a 77-8-9 LWB Super Cab that foot or so of extension was an ideal "flanging point" to make the splice at.
Oh Well, Who Knew, Huh?
FBp .. ... ....
