I really doubt it's something inside the engine. Did you try and remove the heatshield. Alot of times these rust out and end up vibrating quite a bit. Happened on my other engine (D16y7) so I just pulled it off. Also... do you have an aftermarket air intake system??? if so you should check to make sure it's not touching anything else in the engine bay that it shouldn't.
And by the way.... how do you like your ride other than the vibration. I bet that thing hugs the road like nothing else with the 4ws. I've been looking to get one for a while now but all the ones I see up here in Canada all have too much rust for my liking. I may go down to the states to pick one up later on.
Good luck finding the rattling noise.