I have removed the rear strut assembly.  Now that it's removed, can I remove the the stub axle by pounding on the nut after removing the companion flange?  OR, do I have to use a slide hammer attached to the four studs?

I would not beat on it! Slide hammer from the outside but better done while on the car or set it up in a hydraulic press and push it out. Press is my preferred choice

Should you? No. Have I? of course. thread the nut on all the way. use a piece of hard wood to beat on, use a heavy hammer (2lb min), solid support for the strut. If you can't hit straight and hard, don't do it.

How do you set up your press?  I’m not sure how I would apply the pressure.

Like this:

Note that the square-ish wheel hub is hanging free between those two support bars.

The axle is usually not in there real tight. Doesn't take a lot of force.

3 hours ago, wadelester said:

I have removed the rear strut assembly.  Now that it's removed, can I remove the the stub axle by pounding on the nut after removing the companion flange?  OR, do I have to use a slide hammer attached to the four studs?

When my friend (and long time Z mechanic) worked on my wheel bearings, he left the nut on enough to protect the threads and used an air hammer on the back side. That worked well for the left. The right did not budge. He attached a slide hammer to the right, and it still did not budge. Then I used the slide hammer while he used the air hammer. That worked. The threads were protected, too. 

Mind you, this was done with the parts attached to the car.

10 hours ago, wadelester said:

I have removed the rear strut assembly.  Now that it's removed, can I remove the the stub axle by pounding on the nut after removing the companion flange?  OR, do I have to use a slide hammer attached to the four studs?

Since you are asking the question, can we safely assume that you did not upgrade the disk brake conversion bracket?

Everything on the (pictured) rear suspension looks crusty, except for that nice new bracket.

Was there any grinding or other noises observed while the car was in motion?

@wal280z The PO did the disk brakes.  I didn’t know it until I go into the rear end; PO never mentioned it.  My task is to rebuild the entire rear end, so it should clean up nicely.  I couldn’t get the spindle lock pin out so I had to take to machine shop....arghh.