If the transmission and clutch are working properly...its probably not either of those.
Lots of things under the hood can rattle but some things I would check are: Engine mounts, sway bar end links (I would recommend Massive's as a replacement), sway bar bushings (under the car on top of the subframe).
More detail about the noise may be able to help pin-point it better.
2004 SVT: bewst'd!
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2013 Escape SEL 2.0 Ecoboost 4WD
2004 F350 6.8L V10
1986 XR4Ti 2.3L Turbo, 15 psi