I think the term independent is key here. Unlike three jaw or six jaw universal chucks, the jaws in a four jaw chuck are meant to be independent of each other, so there is no need to match them to each other. Also, the purpose of the 45 degree cuts on the side of the jaws is to provide clearance around the work piece. There is no need to true them up, except maybe for aesthetics. I clean mine up once in a while on the belt sander to make them look better. In the case of a universal chuck, if the inside of jaws has become worn they can be reground, but first they need to be clamped on the inside of an accurately bored ring to pre-load them. This will remove any play between the jaws and the scroll plate so they don't move around during the grinding process. It should be noted though that the scroll will wear as well so even re-ground jaws may not run true at all diameters.
Any radial runout of the chuck body can be corrected by loosening the chuck mounting screws and indicating the chuck body on the backing plate. Grinding the radial surface of the body is not really necessary except for aesthetics as with the clearance cuts on the sides of the jaws. What is necessary is getting the backing plate to run true axially. That can be accomplished by grinding or turning the mounting face as you did. It is doubtful that the mounting face on the chuck body itself was not true. Those are normally Blanchard ground at the factory so the front an rear faces are parallel. You may want to remove the jaws and run an indicator on the front face of the chuck to be sure it still runs true after you ground the back face.
Good job figuring out all the different set-ups, especially mounting the chuck backwards on its own backing plate. Figuring out good set-ups with the equipment available is what machining is all about.