It does sound like it may be down a cylinder. Is the check engine light on? If so, it needs to be scanned for trouble codes. If you don't have a scanner, most auto parts stores will scan for free.
If the green eco light remains off all the time, the VCM is deactivated. Has the ATF been changed? If not, I recommend a 3 x drain and fill using Valvoline MaxLife ATF. This can be purchased at Wal-Mart for around $18 a gallon. Do one D&F and drive until engine and transmission is warmed to operating temperature, do the 2nd. After 100-200 miles + I'd do a 3rd. The transmission will be about 80% fresh fluid.
Other things I do to keep a smooth running Honda V6 engine....,
- VCM disabled ✔
- Air filter New/Clean, installed correctly
- Air intake tube leak free, clamps tight
- Clean the Mass Airflow Sensor (MAF), unplug, remove, Using CRC Electronic Cleaner or MAF Cleaner, spray a few short bursts directly into the visible electrodes to knock the dust off, let dry thoroughly before re-installing.
- Spark plugs New/Clean, NGK Laser Iridiums (OEM) or Ruthenium HX. (These engines are known to misfires on other brands)
- Spark plug tubes oil free, If oil is present, replace valve cover gaskets grommets and spark plug tube seals, (I'd replace the plenum/intake gasket when doing this job)
- Coils tested, oil free, replace any oil soaked boots
- Replace PCV
- Replace EGR valve (last resort, high milage with unexplained rough idle
- Use 0w20 full synthetic oil, no semi blends or extended performance oil
- Use Top Tier 87 octane fuel or use injector cleaner regularly
- If primarily driven in the city, take the vehicle on some long highway speed drives