Desktop icons not responding on first click, opening other icons

Ran Tweaking.com's Windows repair program again the right way, but no improvement (plus, even unchecking file associations it still changed a bunch and left me with some reset permissions that have to be changed).

Here's the Task Mgr screenshot in idle you requested and it shows something very not normal I hadn't realized is going on: Windows Explorer (explorer.exe) is running hot. Normally (last I paid attention was with 1511), it idles at 1-2%. I took that shot about two minutes after start up, with no Apps running but Task Mgr (apps show up top). As I write, it's nearing 15 minutes and it's still running the same way. Perhaps that's the clue we've been looking for to understand what's going on with the icons and why XYplorer sometimes goes not responding. I've added a System Explorer screenshot (~2350 handles). I also just turned off and disabled Windows Search, which I didn't realize had been reenabled, but that's not changing anything with explorer. I did run ESET and Trend Micro's scanners and they came up with nothing except a couple false positive PUPs.

Mm, if consistent, that's odd.

1. Please also try to get a screenshot like that just after you've clicked a desktop shortcut as I described previously - I don't know if that will tell us more, but it's (relatively) easy to do although you may have to try a couple of times because of timing.

2. Download and run Sysinternals Procmon (free). This captures all activity, and can filter (technically complex) the result.
Here I'm hoping that since explorer is the dominant process, that capture will give some idea what its doing.
Post a screenshot of anything interesting in what's captured.

You can try that in both idle and after clicking a shortcut.
In the latter case note the exact time you click the shortcut, so you know where to start looking in the captured result.

Note: the capture is LONG, so spend a while looking through. It may or may not help.

3. Now it's time to check at a basic level.
For reference, boot to safe mode, and check near 0 CPU use.

4. Now use msconfig (which you can set up in Safe Mode) to do a clean boot.
Clean Boot - Perform in Windows 10 to Troubleshoot Software Conflicts
(1st part)

Please post a screenshot of the task man.

Please use the numbers above in your reply to make it easier to follow - thanks.

Note: you can organise the display- put highest CPU use at top by clicking the CPU tab.

Procmon.. it depends if anything stands out. If not, move on to the other steps. Obviously the information is there, accessing it is another matter, unfortunately.

I understand you to have noticed there's no change in explorer CPU use before and after clicking a shortcut, so we're down to why that CPU use is occurring.

A clean boot and comparison with Safe mode allows the possibility of a process of elimination of cause- assuming you can reach a point where explorer is NOT using so much CPU time.

Ok, so proceed to clean boot. That Safe Mode (magically?) works suggests you have a chance of finding the culprit by elimination.

Ok, so now you know something. Windows is not fundamentally damaged (Safe Mode ok).
Your clean boot => the same problem.

Now a clean boot is NOT the same thing as Safe Mode. For example, your graphics driver is running.
And if you inspect what is running, you will find a number of of other services as well.
So what you can do is reduce what starts up further.
Inspect the msconfig options, and see what other options there are.
Examine your running processes and services. What is not Windows- can you disable these?
Have you disabled context menu options?

Before the idea was to set up and run the clean boot in Safe Mode

No, as stated that's a misconception. 'run the clean boot in Safe Mode' doesn't mean anything.
You can set up a clean boot whilst in Safe mode, then restart.
Or you can set up the clean boot whilst in Normal mode, then restart.
Same result.

Now the other major clue was explorer's CPU use. So keep an eye on that.

Sysinternals Autoruns (run as admin) lets you disable many other things.

Take due care- best to create a restore point or even a disk image before making all these changes, so you can get back to where you were easily and definitively.