If the flywheel or auto trans counter weight had come from an early engine, it would have come with a nut locking plate. A soft steel washer that you fold up along a flat of the big nut after the nut is torqued.
There is a pin sticking out of the counter weight that prevents that washer from turning. It is just a hair shorter than the washer is thick. The washer was always a bad idea for a number of reasons and was dropped along with the pin and hole. If the pin is still installed in this counterweight, it will prevent the nut from seating fully. This (in itself) will not show up as the nut not fully engaging all of the threads. But look for the pin. If it is still installed. Sand it below flush with the surface of the counterweight. Put one drop of red Locktite on the face of the nut and torque it up again. Turn it over if it has been scarred by the pin. There should be a thread or more showing through the nut after it is torqued up. I would lap the counter weight onto the taper on the crank with valve grinding compound the next time the engine is apart.
If the crank had been used in a racing engine you might find that the crank has been shortened about 1/8" and perhaps a similar amount is missing from the nut. This would be done so the center from a small diameter clutch pack will not touch the crank or nut.
You could check the runout of the surface just out side the bolt holes in the face of the counterweight. It should be very true. If it wobbles a bit, remove it. Use a puller that pushes only on the end of the crank and threads into the bolt holes. Never pry on the counter weight. They are quite flexible and can be bent.
Also the prying will bend the thrust plate and ruin a thrust bearing. Leave the nut on the crank but with a small space above the counterweight, so when the taper lets go the puller and counterweight don't leap into the air and home in on you toes. If you didn't use a factory puller, or the racing beat puller to take your airplane engine apart. You may assume that the thrust plate is cone shaped and the thrust bearings will fail in short order. Even if it is now dead flat, it is ruined. The only piece of a thrust set that is not damaged is the spacer. Discard everything else.
Old thrust plates may be brazed to the bottom of common oil squirt cans to keep them from falling over.
The only use I have found since 1980.
Lynn E. Hanover
In a message dated 5/8/2008 7:40:23 AM Pacific Daylight Time, echristley@nc.rr.com writes:
I torqued down the flywheel nut last night to 300ft.lbs., but I notice
that about 2 threads of the nut are not engaged. It looks like the
flywheel taper is seated completely, but I've never known of a properly
assembled threaded structure having part of the nut sticking out. Do I
need to pull this apart and see what is amiss, or is all as it should be?