Hey Mark72, on those drives, I'm not sure when you say you are going to rebuild them if you just mean service them or reseal them or complete disassemble and refurbish. But especially with the rebuilt one, just pressure test and if no leaks occur then run it. Same with the u joints if they move in all directions with smooth motion run it. Drives need to be removed and serviced every year so there is plenty of time to catch problems developing with proper service and attention. To change out all the seals and u joints when the drive is still serviceable is wasting your precious time and gas money. Throw those u joints you have on hand in your parts storage and fear not you'll use them in the future.
If you do intend to reseal the unit keep in mind that all the bevel gears need to be shimmed so that they mesh properly. Improper depth on any one gear will do significant damage to the set in short order. You need to know exactly what you are doing when reassembling the gear boxes. As for the retainer nut you are asking about above I would advise if you are not seeing any leaks just walk away. Even that top gear case cover has shims under it to preload the upper drive shaft bearings.
If you are just servicing the drive then change the oil, impeller and pump housing liner and go have fun. In coming years check the bellows, the bottom plug magnet for debris, look for milky contaminated oil. You can also send out a sample of oil for analysis for trending.
One aside, when you are running into stuck fasteners apply heat (propane, O/A needs to be handled with great care) to the aluminum you'll find they come out with much less fuss... and breaking.