You shouldn't need a "rebuild kit". Give 'em a good cleaning and make sure all the passages are clear and you should be good to go.
Jetting changes will be based on what you want to do. If you're just drilling holes in the air box as well as the exhaust, no real change is needed as it makes a negligible difference.
Now if you're adding pods and a full system that is a different story.
2013 H-D FXS Blackline
2006 V-Star 1100 Classic
1980 XS650 Bob (in progress)
USMC - 0331 - OEF