Best way I have been able to determine how to tell based on posts: Start it from cold. Since the auto is a wet sump, the hydraulic lifters should almost immediately fill and you MAY hear a second of a sound that is "similar" to marbles in your engine somewhere (valves tapping etc). If it continues sounding like marbles for a 30+ seconds, then we have an issue.
Duoselect/dry sump cars will hear the sound for 3-4 seconds at most, but it will be much more obvious.
Transition for VVT takes place over 4000, so 2-3k doesn't seem likely to be related to this. Probably just needs a computer reboot (seriously) to get it to work a bit better. Unplug the battery overnight and try again the next day. You would need the code to unlock the radio.
Make sure you run through the proper startup procedure. Turn the car on but do not run the motor, let it sit for 1 minute, then start the car and let it sit for one minute while doing nothing. This will have the car figure out the valves, throttle body etc. Only has to be done when you pull the power as per the service manual.
If that isn't it, probably spark plugs, though I doubt it at 29k miles. Well it COULD be, though it is more likely that if you drive it REAL hard for a few minutes it will resolve itself, after trying the above. These engines don't like to be driven lazily all the time,