I wasn't gonna say anything..
I wasn't gonna say this, but after compulsively reading this, I just gotta.
My 04 has, since new, rattled like crazy on startup, then settled to its properly cacophonous symphony of mechanical bliss before it's even warm enough to drive. It still does. All the pre-06 ones that I've been around do. It doesn't bother me. In fact, I like the clackalacka better than the constant whirring of the later bikes. Not that it ever bothered me riding my friend's 06 around Idaho. I reckon it's just different ways for engines to be.
IIRC, the startup racket started bothering Pyndon, and he described updating to 06 cam-train and uprating the oil pressure thing in his epic maintenance thread.
If it really bothers you, there's your fix, but I'm not convinced the noise means anything is wrong. If mine blows up I guess you get to laugh.