For the roller rockers you likely have to file some aluminum off for proper clearance of the rods. If the engine is apart for the cams it is easier to make sure you get all the filings as you have full access to the top and bottom. It is easy to file the edge just a bit messy.
Are you referring to filing of the rocker pivot mounts? Or perhaps filing of the pushrod opening in the head?
I see in the S&S catalog that the roller rocker kit includes new pushrods, but I also see the stock length pushrods work with any cam. So are the new pushrods included with the roller rockers physically different (longer or thicker) in some way to cause a clearance issue?