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.
'10 Ford Escape 3.0 V6
2004 F350 6.8L V10
'86 XR4Ti 2.3L Turbo
'07 ST ; formally bewst'd - R.I.P