It wouldn't create enough vacuum to be measureable by any means, but it would tend to induce turbulence. I'm not up-to-date on the Exploder intakes and whatnot, but from what you're saying the TB is 65mm and the intake's TB mount is slightly larger, hence the taper. I really don't think that's going to make much of a diff if it's functioning the way I think it is. If somehow during the machining process there was a surface removed required for sealing against the TB, I can see how that would make for a vacuum problem. Just take it apart and look at everything closely, you'll figure it out. Good luck.
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Capri306, Moderator, The Mustang Works Online
1979 Mercury Capri, 5.0L -- C4 -- 2.73
1987 Mustang LX Notch