Permissions are all messed up in 10.9

Question

I installed Mavericks 10.9 on my 2008 Mac Pro desktop a couple of months ago. Then the monitors (2 of them) developed odd patterns. Apple Care (AC) tried to help me start 10.9 in Safe Mode, but when the progress bar finished, the computer shut itself off. We could never start in Safe Mode. Then AC diagnosed a hardware problem and recommended an Apple repair shop near me. The the video card was bad and they replaced it. But when they got things running, the permissions were very screwed up. They spent a lot of time repairing them (I don't know how), and then they upgraded the MacHD from a 1.5T Seagate to a 2T Western Digital and cloned the old MacHD to the new 2T drive. I took the machine home and still had permission problems and other problems. Adobe Acrobat Pro would not print PDF files, which I fixed with a suggestion from the Apple Forum. Then Photoshop CS4 gave me a "License Expired" message (Error code 150:30). I fixed that from the Forum (Adobe Community > Downloading, Installing, Setting Up > Discussions: Error code 150:30), with a fix that required a little entry in Terminal ($ sudo sh install_fnp.sh). That allowed me to open Photoshop, but when I turned Photoshop off and restarted it I got the "License Expired" message again.
On the advice of Apple personnel in the Apple Store in Spokane, I unstalled Photoshop CS4 and reinstalled it from the CS4 Suite DVDs, installing just PS with all the supporting apps that the installation automatically chose. Then when I started PS, I got an error "Don't have adequate permission access" or something like that that has been addressed in the Forums. From the Forums, I followed the suggestion of adding "username(me)" to the permissions window of the Info panel of the MacHD and choosing "Apply to enclosed items". That got rid of the "Don't have adequate permission access" error, but I got back the "License Expired" error again and PS wouldn't open. When I tried the "sudo sh instyall_fnp.sh" fix again, I discovered that I couldn't log in to Terminal:
Last login: Thu Feb 20 18:27:35 on console
login(12166,0x7fff7cf59310) malloc: *** error for object 0x7fe65b500180: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
[Process completed]
Meanwhile, using Disc Utility and "Verify Permissions" I see that my Permissions are still totally messed up. So I don't know what to do now.
I also have a Macbook Air. I see that in "Disk Utility > Verify Disk Permissions", the Permissions are also messed up on my Macbook Air, on which I installed 10.9 recently, but it seems to be working ok, so I have just left it alone.
I'm the Administrator and only User on this system. The Permissions remain a huge mystery to me. What is the difference between "Administrator", "System", and "Username(me)"? Should all these be present, with "Read & Write" access? And how do you fix such global Permissions problems?
Can anyone help?
Thanks.

Answer 1

You may need to rebuild permissions on your user account. To do this,boot to your Recovery partition (holding down the Command and R keys while booting) and open Terminal from the Utilities menu. In Terminal, type:  ‘resetpassword’ (without the ’s), hit return, and select the admin user. You are not going to reset your password. Click on the icon for your Macs hard drive at the top. From the drop down below it select the user account which is having issues. At the bottom of the window, you'll see an area labeled Restore Home Directory Permissions and ACLs. Click the reset button there. The process takes a few minutes. When complete, restart.   
Repair User Permissions