You'll find even after spark plugs a few thousand Km's later the problem will return, I suggest upgrading to Splitfire Coil Packs to be honest, when i had the RB25 in my R34 it used to play up and the 6th cylinder wouldn't work due to faulty coil pack, i replaced it and then it was perfect. The check engine and traction control light would come on also when this happened, and usually restarting the car would fix the issue, or if I needed to, I would pop the bonnet, and unplug the coil pack then plug it back in.
Next time it happens you can find out which coil pack it is by un-plugging them one at a time and when there is no change in one of them (still runnning rough), there's the faulty coil pack.
I'd also be inclined to say your ODO reading is genuine and accurate, most R34's have rather low Km's, mine had 29,000 when I purchased it a year ago. You're R34 is nice and clean btw, good buy.
Cheers,
Dallas