I have a similar or same thing happening in my 2001 2.7 5-speed, and since I haven't fixed it yet I can't be quite confident really at all what it is, I can say I've ruled out a bunch of things I've already tried and looked closely at.
First off, the noise only happens when engine is warmed up (or even better yet, HOT), is much more pronounced the more the throttle, (needs to be really hot to do it free-revving, without any loading), and also only in a certain rpm range (and in multiple, dint inch resonance bands within that range). Seems to be in the 2000-3000 rpm area, maybe three peak resonance bands in there about 200 rpm or so apart. Sound is a metallic rattle, sounds just like a rattling heat shield, most noticeable when driving by something reflective and with the top down. Seems to be coming from the passenger side. At first I thought it coming from back, but further diagnosis, indicates it coming seemingly from up by the motor, much higher up, perhaps up near the exhaust manifold or even above it somehow.
It's been driving me crazy, although not bad enough to stop everything else to fix it, and I've already looked at heat shields (quite a few of them). If not something with the exhaust manifold, I've wondered if could be accessory drive belt (like power steering pump or water pump), or even dual-mass flywheel pieces. I've pretty much ruled out exhaust, though. Problem is when I get it up on jackstands to diagnose it, by then the engine has cooled off enough all I can get is a faint sound if I can get it to reproduce at all. Same goes for removing the top or front engine cover. Sorry I don't have the answers, but at least know you're not alone.