I just asked Van's that same question, as I am ready to disassemble the forward section also, and the directions say to remove the F-770 side skins, do all the prep stuff, then reassemble and rivet, without mentioning separating the center and rear sections. Ken's answer was to separate them and prepare the holes at any time prior to final assembly. That is the answer I expected, but it just seemed like a pretty big thing not to mention, at least to me.
I also asked about putting the WD-721 landing gear mounts in place temporarily at this point, to check the holes in the F-772 forward bottom skin for fit around the landing gear mount penetrations (7A only), since if the holes need to be trimmed to fit, it would be easier to do it while the fuse is still inverted and the F-772 skin is still removable. Ken said that was OK too.