how to reinstall catalina clean

I don't know what stores that information, so I don't know if just reinstalling will clear out the info.

Maybe just try a Safe Mode boot to clear the system caches.

Once booted, restart normally.

The OS doesn't get damaged unless you damage it with system modifications including "cleaning" or "protection" software.

In Catalina, the OS is installed on a separate Volume that is mounted Read Only. That is why it pretty much cannot be damaged.

Your data and third-party system modifications are installed on the - Data volume.

Permission problems would only result from a failed migration or incorrectly moving files into the home folder.

What is the manifestation of the permission problems?

You may be able to determine what is causing the problems by running EtreCheck and posting the report here for us to look at.

Use the Share Report > Copy report button to copy to the clipboard. Paste it into the Additional Text area in a reply, here (document icon).

If you want to "clean" install the OS, boot into Recovery and erase the Macintosh HD volume, then reinstall macOS.

The report indicates the system is running well since it said performance was excellent; however,

Here's a first clue:

System modifications - There are a large number of system modifications running in the background.

You are currently running an older OS version:

macOS Catalina 10.15.2 (19C57) 

You have these system modifications installed:

Kernel Extensions:
  /Library/Extensions
    FTDIKext.kext (1.0 - SDK 10.14)
    Dropbox.kext (1.12.2 - SDK 10.14)
    Wacom Tablet.kext (Wacom Tablet 6.3.11-3 - SDK 10.10)

They may be necessary to you, but they will necessarily destabilize the OS.

Are they the most current versions?

If you choose to erase the startup drive and reinstall the OS, you will get 10.15.6. If you held back for some reason, you will not be able to go back to 10.15.2.

As the system modifications are not on the actual startup volume, you would need to erase both the Macintosh HD and Macintosh HD - Data volumes, the migrate you user data from your backup.

I would not install anything until you verify the system is running fine, then add each necessary modification one-at-a-time to determine if they are the cause of your problems.

What about the prompts for keychain access?

Is it continuous? Does it not remember when you allow it?

FTDI appears to be a USB bridging solution to use devices connected via USB to act like it is a COM port.

save your data first. command + r or option command +r. Then Disk Utility and delete both Catalina volumes. Then add a new Volume and name it then proceed with the Catalina install.

No idea why you think this is a problem. Does it constantly recur?