Could be nearly anything actually. My car seems to have this weird rattle at around 1500-1800 rpm, but its something in the body.. (plastic or whatever). 3k rpm sounds like either 5th gear, motor mount, cv joint or something like that, since you say when you apply torque, thus adding pressure it goes away. You sure its not bad tires or alignment? I would think that if fuel was off and/or timing, that low rpm idle would be rougher.