On my e99 they weren't connected together at all and after doing the H&H I have found the front vent leaks
It looked molded in to me and I'm thankful you confirmed it before I did the same thing.

I think either setting it up like Sous or running it as jhl3 has should work too. I'm getting tired of putting fuel on the ground and need to fix it...

 

Putting fuel on the ground is why I took it apart. Just wanted to make sure the two lines didn't meet in the middle with a vent can or something. If they did leak, fuel would be trapped in the larger line in the middle unless it got sucked back in some how. Can't believe how cheap these vents were made. The vents for the steel tanks are much heavier. At least the ones I bought from Ford. Hope they take them back!

 

Bonanza,
I'm just finishing up the Hutch mod on my 2000 F250 and it sounds like you and I have the same tank configuration. I ordered a new foot for mine and did measure the depth of my old pick up as best I could, it had broken off and was lying in the bottom of the tank, it was ~ 15 1/2" between the bottom of the top plate and the bottom of the pick up. My new assembly measured 15 1/4" when I got done with it and left me ~ 1/4" of clearance off the bottom of the tank. The two short vent tubes on my tank are capped as you described and aren't leaking, yet, we'll see when I get it running tomorrow or the next day. I went with the Racor PS 120-1 with barbed adapters that were 1/2 X 3/8 and will be mounting it tomorrow. I don't have any worries at all about this setup.
Like you said the inside filler and vent tubes that lead to the fill port are set at an angle close to the top of my tank. I decided, like you, to forgo the harpoon mod as I haven't had any problems filling my tank. It only holds between 34 and 35 gals. no matter how you fill it, that's plenty for my needs.
Good luck with your project, I'll let you know if I have any problems with mine so we don't both make the same mistakes.
Lewis