You pretty much answered your own question. As you said, the engine could not possiblity be original to the car and preserving a correct numbers-matching part is only important if you are trying to maintain a completely numbers-matching drivetrain. No reason to waste $$$ fixing the original for the YD.
The E-brock manifold is pretty much a copy of the RA IV manifold but in aluminum, so you are good to go.
2012 Mustang Boss 302 #1918, Competition Orange. FGF replacement 2006 Mustang V6 Pony, Vista Blue. Factory ordered. 2019 BMW X3 (Titled to the wife, but I'm always driving it for her. So I'm claiming it) Old projects, gone but not forgotten: 1967 FB 400, original CA car. After 22 years of work, trashed by the guy who was supposed to paint it. I had to sell it. 1980 Turbo Trans Am 1970 Mustang fastback, 351C 4Bbl, auto 1988 Mustang GT, 5 speed 1983 F-150 4x4, built 302 1994 Chevy K2500 HD 4x4, 454 TBI