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As far as using the fuel conditioner, do I just pour in the recommended amount into my tank (with what I assume is fuel that has ethanol in it) and just let it sit or is it a good idea to run the bike to get conditioner through the engine?
You want to make sure the conditioner is mixed very well with the fuel. The best time to put it in is after refueling when that last ride of the season is done. This ensures that the conditioned fuel is in the fuel lines and injectors -- or carb bowls and internals for other such engines.
If you store the bike with fuel you want the gas tank to be full so there's very little air within. This reduces the amount of condensation that will form on the parts that are exposed to air (e.g. top & sides of the tank) and thus reduce the amount of water that coalesces at the bottom of the tank (water is about 2 pounds heavier than gasoline). Your other option is to drain all fuel and run it dry so there is none remaining but I wouldn't recommend this unless the engine is going to be stored for a year or more.
Side note: On my outdoor equipment, like carbed leaf blower and lawn mower, I run them dry when their season is over to ensure all fuel is gone from the system. They're smaller, simpler, and easier to do it to. Remember, running an electric fuel pump dry for too long isn't good for it as the fuel lubricates and cools the pump.
In my opinion, I do not recommend running the bike (or any other engine) for a few minutes every few weeks. If the fuel is conditioned and the battery is on a tender then it'll be fine. Running an engine without bringing it up to operating temperature is not good for it
over time and it really does nothing but create additional wear-n-tear. In all my years of air-cooled engine experience there has been
zero evidence that periodically running an engine for a short, non-operational time, is beneficial to it. Now, if you have the opportunity to actually ride, to bring the engine up to operating temp, and ride it for several minutes afterwards, then go for it as that's fine because the engine is in its zone and parts are meshing as engineered to, moisture is being driven out, seals are being properly lubricated, etc. Just make sure the tires are at the proper pressure
