When I put my Holley throttle body in on my XE, I had to push the intake mainfold out 12.5 mm to allow the Redline adaptor to fit. Then the new gasket woudn't seal because the rocker cover (steel, not the spunky EFI number) was hooking up on the manifold. Check this first, then follow Ford shop practice.
Ford engineers have some bizzare hoops that you must jump through in there service manuals...mainly because they want to save on warranty claims. They do care, but sometimes their arms are too short and the corporate coffers are too deep to reach! Gaskets, auto trans servicing for BW 35/30/55's, thin-wall block bores on V8's, power steering pumps, too small cross flow radiators, disc brake axles on 1973-1979 heavy duty diffs, BW cone clutches on LSD's....all of them penny pinching items that Merceades Benz, BMW, even Opel and certainly Toyota wouldn't have let out of the factory if they were in Fords situation. Ford just put caution warnings and service notices out.
Ooops, got carried away again. At least if my Falcon breaks, I can fix it. A MB E-class would send me broke before I even paid for it!