The system is heavily modified by third-party software. Each such configuration is unique and unpredictable. I can only guess which of the many modifications may be contributing to the problem. As a start toward solving it, I suggest the following steps.
A
Some of your user files (not system files) have incorrect permissions or are locked. This procedure will unlock those files and reset their ownership, permissions, and access controls to the default. If you've intentionally set special values for those attributes, 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.
Please back up all data before proceeding.
Step 1
If you have more than one user, and the one in question is not an administrator, then go to Step 2.
Enter the following command in the Terminal window in the same way as before (triple-click, copy, and paste):
sudo find ~ $TMPDIR.. -exec chflags -h nosappnd,noschg,nosunlnk,nouappnd,nouchg {} + -exec chown -h $UID {} + -exec chmod +rw {} + -exec chmod -h -N {} + -type d -exec chmod -h +x {} + 2>&-You'll be prompted for your login password, which won't be displayed when you type it. Type carefully and then press return. You may get a one-time warning to be careful. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
The command may take several minutes to run, depending on how many files you have. Wait for a new line ending in a dollar sign ($) to appear, then quit Terminal.
Step 2 (optional)
Take this step only if you have trouble with Step 1, if you prefer not to take it, or if it doesn't solve the problem.
Start up in Recovery mode. You may be prompted to select a language, then the OS X Utilities screen will appear.
If you use FileVault 2, select Disk Utility, then select the icon of the FileVault startup volume ("Macintosh HD," unless you gave it a different name.) It will be nested below another drive icon. Select Unlock from the File menu and enter your login password when prompted. Then quit Disk Utility to be returned to the main screen.
Select
Utilities ▹ Terminal
from the menu bar. A Terminal window will open. In that window, type this:
resetp
Press the tab key. The partial command you typed will automatically be completed to this:
resetpassword
Press return. A Reset Password window will open. You’re not going to reset a password.
Select your startup volume ("Macintosh HD," unless you gave it a different name) if not already selected.
Select your username from the menu labeled Select the user account if not already selected.
Under Reset Home Directory Permissions and ACLs, click the Reset button.
Select
▹ Restart
from the menu bar.
B
Back up all data.
Run the following command in the same way as before. It moves to the Trash "semaphore" files that have not been cleaned up by the system and may be interfering with normal operation. The files are empty; they contain no data. There will be no output this time.
find L*/{Con*/*/Data/L*/,}Pref* -type f -size 0c -name *.plist.??????? -exec mv {} .Trash/ \; 2>&-Log out or restart the computer and empty the Trash.
C
Please disconnect the Thunderbolt drive and see whether stability improves.
D
Please back up all data before proceeding.
Launch the Font Book application and validate all fonts. You must select the fonts in order to validate them. See the built-in help and this support article for instructions. If Font Book finds any issues, resolve them.
Start up in safe mode to rebuild the font caches. Restart as usual and test.
Note: If FileVault is enabled in OS X 10.9 or earlier, or if a firmware password is set, or if the startup volume is a software RAID, you can’t start in safe mode. In that case, ask for instructions.
If you still have problems, then from the Font Book menu bar, select
File ▹ Restore Standard Fonts...
You'll be prompted to confirm, and then to enter your administrator login password.
Also note that if you deactivate or remove any built-in fonts, for instance by using a third-party font manager, the system may become unstable.
E
The test results show other issues, probably not related to the original question.
The following Safari extension(s) is/are malicious and should be removed in the Extensions pane of the Safari preferences window:
Lunaticake
F
You installed the "Malwarebytes" product, which failed to remove the malware. That's what you should expect from such products: failure. I suggest that you remove it according to its developer's instructions, and never install any "anti-virus" or "anti-malware" product again. Relying on software for your security is a dangerous mistake. The only real security lies in safe computing practices. Ask if you want guidance.
G
You downloaded an application called "RcEngMgr" that could be used to control the computer remotely. If you granted remote access, and you're not absolutely sure you can trust the party to whom you granted that access, ask for instructions.