Not sure where you guys are getting the three inches more on top theory. Both the Sherman and the Aero are designed to go right up to the body pan, and touching it if the installer desires.
The Sherman is adjustable that way of course, but the Aero is typically ordered for use with, or without a particular amount of body lift, so that the tank sits as high as possible between the rails.
Custom ordering lets you fill whatever extra areas there are, but that's only downward and/or forward. Adding some downward in your case, because clearance is not likely to be an issue, is a sure way to get more fuel. I would personally push it out forward of the crossmember as well, to gain just that much more. Like the Sunset Metal tank is.
So what overall height did you settle on mofoco? And what capacity does it work out to?
Oh, and as far as the return, since this is custom, add your own wherever you want. And tell them to leave out any other EVAP vents while they're at it.
Personally again, I'd have them in any tank. Should make filling easier, and should make it less likely to fumigate the garage. But if you're not having any trouble in that regard now, I can see why you'd like to leave them out.
Good luck. Let us know how it goes.
Paul