All of my favorite multiblock presentation (in handbook) methods use layer-by-layer step-through. Ars Magica 2 and Immersive Engineering are the only two that jump to mind, but I know other mod authors have done the same thing. IE is even open source, so you could see how they do it. Also from what I recall, those handbooks also provide the name of the blocks when you mouse over them
That having been said, take a look at the way
Schematica presents its schematics in world. As long as the various components are visually distinct even if the alpha is turned down? Something like that would work beautifully. Especially if you presented layer-by-layer, which you could do as simply as cycling through them by right-clicking on the blueprint marker.