Well,i thing you should prefer Dynojet Stage 1 jet kit when you have modded pipes and Stage 2 if you have a good set of aftermarket pipes-open airbox-K&N or BMC air-filter .Putting on a K&N filter or cutting your airbox without putting a jet kit at the same time ,will make your bike run leaner so you lose actually performance. If you put on your bike a nice set of what i told above you will gain a noticeable performance and the sense that your bike is smoother at all RPM range .My opinion is get the job done well or don't do it at all .Hope i helped a bit .
The Factory Pro jet kit is easier to deal with than Dynojet and you don't have to worry about getting stage 1 or stage 2, since everything you need is in the kit. It will come with the right jets if you get the one for your particular bike.
See the FAQ on this site for details on installation.
If I were rebuilding a set of carburetors right now, I would order a new set of needle jets (emulsion tubes) too, while I'm in there. New ones from Factory Pro are supposed to wear better than the stock ones.