I've rebuilt many of those double clutches during my time at a FNH dealer, and can tell you that I have never done it on the flywheel, always on the jig. I don't recall the factory manual even mentioning the flywheel method as an option.
Either one of two things is going on here: 1) You're misreading the dimensions and/or referencing off of the wrong portion of the hub, or 2) (more likely) you have wear on the fingers and linkage parts causing the levers to be farther down (closer to the flywheel) than they otherwise would be.
I would disassemble the plate assy and inspect the parts closely for wear. Pay particular attention to the 6 struts with the oval holes in them. I would bet that they are worn big time.