Not sure how you got the old primary chain off and on without removing the rotor unless you have a split link primary? Never used one of those, mine were always endless but now have a belt drive. If you have the primary and clutch assembled and rear chain in place, put her in top gear and stand on the rear brake or adjust the brake so it's locked the drum. With a 2ft (or more) extension on the wrench a good fitting socket the nut should undo easy. The rotor might need easing off the crank with carefully placed levers. Don't lose the spacers between rotor and crank sprocket and the woodruff key.
The wobble you have from the clutch drum is well known, maybe you didn't notice it before? Mine does it and that's a newish aluminum belt drive part. Usually it's a bent mainshaft and unless it's really bad you can live with it or buy a new one. The shaft has no support beyond the outer sleeve gear bush and it's under quite a bit of stress. You should check the seating of the grooved clutch washer against the shaft circlip, that the circlip is in it's groove and in good nick etc. The clutch centre bearing cannot really be in other than square but check it's condition anyway.
Norton developed an outer support & bearing for the mainshaft in the 70's and I know SteveManey does one, see
www.stevemaney.com but you need a belt drive and modified inner case.