I believe it was Millet that said that those side limbs are important to the development of the trunk, so unless they are a problem in some way, I think I would leave them. Skeet
So is there consensus I should clip them. They are below the graft since there is no longer a graft. I wan the root stock to grow very strong so I can graft it again. Some one told me I could use the other branches as future rootstock as well. What do you think? Or should I just clip them.
I'm not sure what rootstock you have, it is certainly not a trifoliate. It could be an edible fruit that was used as a rootstock, it has fairly wide petiole wings, so it is not lemon. Maybe someone else can ID it. As for the side branches, if you are going to graft, you can use them for different varieties if you want a cocktail tree.