Losing use of applications one at a time

Question

This is an expansion of an earlier question that has not been resolved:
"10.9.4 Permissions disorder?"
My configuration:
OSX 10.9.5, Mac Mini 2.6 GHz I7, 16GB RAM, 1TB disk, several external USB disks on hubs. All software is up to date.
The machine is degrading by the day. I originally suspected permissions problems, and the Terminal "resetpassword" solution that was proposed has not worked. However, most of the failures I will report below seem to be consistent with applications being unable to write. Here are the details, organized by the applications that are failing:
Chrome was failing to launch (in my account only; my wife's is OK) but I fixed that by finding the hidden Application Support folder, deleting and reinstalling. So far, Chrome is working OK.
Preview: When I open the app I get the alert: “The file “Untitled.pdf” couldn’t be opened because there is no such file.” When I clear the alert two formerly scanned and printed but not saved (both untitled) pdf files show up. I can close them without saving, but they come back every time I launch Preview.
Safari: 1.On every opening I get an alert: "Your Safari extensions have been migrated.” 2. Bookmarks are not remembered in the Favorites Bar after quitting. 3. No history has been saved since August 14, 2014.
Text Edit: Autosaving sometimes leads to this alert: “The document “<document name>” could not be autosaved. The file is locked.” “Save  Anyway” fails the same way. File>Duplicate creates a file that can be saved. To get rid of the original document that can't be saved I have to force kill the app.
TextWrangler: Attempting to quit with an edited document fails with the alert: “This operation couldn’t be completed because an error occurred. You do not have sufficient privileges to perform this operation (MacOX Error code: -5000)” I must force quit. Reinstalling (even after deleting Application Support folder) doesn't fix problem.
System Preferences: The System Preferences>Sharing>File Sharing window is often open when I boot into my account. I have not selected the option to reopen windows when shutting down, and this window was not open when I shut down.
iTunes/iPad: 1. Alert during sync: “Attempting to copy to disk ‘’ failed. The required disk cannot be found." 2. Concurrent alert: "iTunes could not back up the iPad <iPad name> because the backup could not be saved on the computer. Please disconnect and reconnect the iPad, then try again". 3. Synciing hangs on step 8 of 8: “Syncing <iPad name> (Step 8 of 8) Preparing to copy items" (The iTunes folder is on an external disk with ownership ignored and read/write permission.) I have attempted to switch to iCloud backup but it doesn't respond to my request, so I cannot either sync or back up the iPad. I've restarted as advised, to no effect. (The upgrade to 8.0.2 fails during the backup.)
I recently reperformed the "resetpassword" routine on my account and the root account, to no effect.
The problem I reported earlier that my laptop can't write to the mini using file sharing persists.
Suggestions, please.

Answer 1

Back up all data before proceeding.
This procedure will unlock all your user files (not system files) and reset their ownership, permissions, and access controls to the default. If you've intentionally set special values for those attributes on any of your files, they will be reverted. In that case, either stop here, or be prepared to recreate the settings if necessary. Do so only after verifying that those settings didn't cause the problem. If none of this is meaningful to you, you don't need to worry about it, but you do need to follow the instructions below.
Triple-click anywhere in the following line on this page to select it:
sudo find ~ $TMPDIR.. -exec chflags -h nouchg,nouappnd,noschg,nosappnd {} + -exec chown -h $UID {} + -exec chmod +rw {} + -exec chmod -h -N {} + -type d -exec chmod -h +x {} + 2>&-
Copy the selected text to the Clipboard by pressing the key combination command-C.
Launch the built-in Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.
Paste into the Terminal window by pressing command-V. I've tested these instructions only with the Safari web browser. If you use another browser, you may have to press the return key after pasting.
You'll be prompted for your login password, which won't be displayed when you type it. Type carefully and then press return. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
The command may take several minutes to run, depending on how many files you have. Wait for a new line ending in a dollar sign ($) to appear, then quit Terminal.