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If you increase the air flow, then you need to increase the fuel delivery or the bike is going to run leaner and hotter. Take a copy of your current MAP and install a new MAP for your specific application, or, modify the existing MAP and add more fuel to it. Other things you can do to cool you and the bike down is :-
1. Add a Jagg 10 row oil cooler.
2. Remove the lowers.
3. Change to a 2-1 (pro-pipe) to get rid of the Y.
4. New MAP (as above).
Your loss of back pressure increased reduced your low end torque, increased air flow making it run leaner. A new map will help run cooler but probably will not do anything to add low end torque.
Have you tried some of the maps on the Power Commander site? You can try a few that are a close match to your set up and see if one of them will do the trick. They are free for the pickin', and you can always adjust some of the settings.
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