I never recommend anyone's jetting kits. I think you're better off using OEM Keihin parts, whether through Yamaha or through a dealer such as Sudco.
Have you taken the time to prowl through the jetting DB? http://www.thumperta...tting-database/
Also read: http://www.thumperta...b/#entry2289879
It is a misconception on two counts that the FMF pipe will automatically require different jetting. The first assumes that the pipe is so much more efficient than the stock pipe that it will need it. The fact is that stock YZF pipes (not including the "shorty" on the '08-'09 models) are really pretty good pipes top begin with, and the FMF will probably add no more than 1 full HP.
The second error in thinking is that the pipe "is going to be pulling so much air out" that you'll need to go richer. Carbs work based on air velocity and the vacuum produced by that air flow on fuel passages with fixed orifice jets in them. If the air flow through the carb increases, more fuel will be delivered, simple as that. If the increase in air flow is great enough, it will increase the strength of the vacuum signal at the main jet so much that it will result in the mixture becoming too RICH, not too lean.
Put the pipe on the bike, see how it runs, and go from there. Don't get ahead of yourself.