RE: lap joint in molds
You generally make an additional piece (or set of pieces) for your joggle mold after the primary mold parts are built. The "joggle tool" is then removable and the parts can still be joined using the molds and alignment pins.
There are several ways to get the correct offset for the joggle tool. I hope other folks will chime in with suggestions, since I've only done it one way. I used the same plug without modification to lay-up my joggle tools, then shifted them inward (towards the center of the part) by the approximate thickness of the part laminate. They were then fixed to the primary mold piece using screws.
HTH,
-David