06 Yamaha Roadstar misses under load

How do you define Chugging ? Engine miss under load ? when shifting into overdrive ?
Have you checked fuel pressure and is the check engine light on ?

run higher octane or octane booster in fuel

all bike are to be checked in the upright position! then find out how much the bike takes from your manual if you dont have a manual ...do the following ..when you just change oil and not filter you will be adding less oil,"almost" all bikes take @ 3 quarts oil minimum, so what i do to be safe!! is always after draining is put in two quarts no problem, but with the third bottle i only pour in half.. drop oil cap back on and start the bike and let it run for a minute, the turn it back off, then check oil level, if it doesn't register anything on the stick or sight glass then your o.k. to add the rest. now take a reading, and only fill to almost full, i always under fill my bikes, because over filling will cause damage to internal bearing by the air bubbles from the splashing of the crank in the oil pan. Same as cars.
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Thanks

Your bike takes a little over 4qts of oil. The engine drain plug is located on the lower left front of the motor. The oil tank drain plug is located on the bottom of the oil tank, on the right side of the bike.
When refilling, put in about 2.5 quarts of oil in the tank and start the bike and run it for about minute and blip the throttle a few times. Then add the remainder of the oil. Run the bike to operating temperature (approximately 15 min) and allow it to idle for about 3 minutes. Then check the level after a minute or so and adjust as necessary.

The Yamaha Roadstar has a dry sump oil system. What this means is that the oil is stored in an oil tank to reduce the size of the engine. By storing the oil in the tank (which is under the seat and has the filler cap/dipstick, the engine does not need a sump under the crankshaft to store the oil. In this type of system the oil is pumped back to the tank after making its rounds through the engine. When you shut the bike off the oil will settle in the engine until you run the engine. The procedure to check the oil is to warm up the engine and allow it to idle for approximately 3 minutes. Do not rev up the motor during this time as it will cause the oil level to not read correctly. After shutting off the motor, check the oil level and adjust it to keep it in the proper level on the dipstick.

check air filter... is it clean? check that you have good fule flow from fule tank,,is filters clear, ,,,strip carb and clean jets,,,check flote level,,if its low raze it,,,change spark plug! it could be miss fireing

Check the spark plugs, they may need replacing.

I had same problem a couple years ago with 95 sl2, i had new wires and plugs instaled and they replaced the valves also. car works great since then...