@Crenda So how about the following:

1) Remove cactus from soil

2) Spray with rubbing alcohol

3) Spray with garden hose and clear off root ball

4) Trim any roots that have died off

5) Replant

I can just leave the bruised/rotting sections and hope those dry out since they were not caused by a fungus?

Your plan sounds like a good one with the exception of leaving the rotted parts. I have always gone by the mantra that rotted (dead) tissue must be removed because it will not get better and will likely spread. That is regardless of the cause.

So I would not be surprised to see other people tell you to cut until there is no discolored/rotted tissue left. Sometimes merely excising the small area will do the trick, other times it requires decapitation to get it all removed. Both the top cap and the stump will survive and grow anew for you if you have to remove the entire center section of your plant. Sometimes we get surprised during surgery and things aren't as bad as they appear.

Here's hoping we hear from some others on this.

@Crenda, doing careful excise work around such a thorny cactus is tough work.

Growing plants is really tough.

Here is a Euphorbia Milii "Crown of Thorns" that is not doing very well. Are these also scales near the top of the plant? This plant was right next to the affected cactus.

Just to document for future readers: I moved the cactus with the scale infestation into the hot sun for the Summer. Those bugs did not like that, and by the end of the Summer the plant was clear of all scale. It is pristine on all the external surfaces now. I did cut the plant in half and tried to save the rotting top section by cutting out the rotted section and replanting it. The entire top eventually succumbed to rot, but the bottom half survives and is growing.

I will probably try to keep these plants in the sun all Winter long and let them endure the rain. Since they are in pure pumice, I hope the chances of root rot are minimal.