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> how much choke and for how long;
With all the variables, the only advice one can give is "however much is required to start and then keep it running, for however long may be needed to ensure it runs smoothly." The procedure you're considering is reasonable, so long as it is ready to run smoothly after two minutes.
> i am considering 2nd gear for anything below 60 km/h and infact i am even considering 1st gear for anything less than redline to help heat up the bike.
That I would definitely not do!
The two conditions that cause maximum wear on engine components are: (a) when the engine is first started from cold, and (b) when the engine is operated at high RPM. Combine those two factors and you end up with worse wear than either alone.
Since you have observed a longer warmup time with the aftermarket filter (probably due to the increased flow of the cold air into the engine) I would switch back to the stock filter for the winter.
An additional option, where feasible, might be to find a longer commuting route so you can be sure of having the engine fully warm before you get into rough traffic. Of course, the additional time may get you yourself more throughly chilled.
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John
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