Permissions Problems PT.II The Empire Strikes Back

Hello all. I initially had a permissions problem with files on my computer after upgrading from Tiger to Leopard last week. I thought I had the problem solved with the doubleteam effort of RodneyW. and V.K. The topic is here:
http://discussions.apple.com/thread.jspa?threadID=1510598&tstart=0
Now all the folders in my Documents and Pictures are fully accessible to me.
A bit of background: when I log into the mac, I am always logged in as an administrator with my username.
Today, I checked the permissions of my applications, and some of them which I installed myself still say that I have 'custom' access, and at the same time showing on the list of users my username with "read and write" permissions!!! Argh!!!!!
Here is a list of programs that I had installed on my computer which are now showing that I have custom access while logged in using my regular username (and I am an admin).
*Application: User/Privilege:*
*Tax program* myusername(me)/ read & write
admin / read
everyone / read
*Bits on Wheels* myusername(me) / read & write
(unknown) / read
everyone / read
Firefox myusername(me) /read & write
admin / read
everyone / read
flip4mac system / read & write
admin / read & write
everyone / read
*Logitech Harmony remote* _unknown / read & write
(software for remote control) (unknown) / read & write
everyone / read & write
Maintenance system / read & write
admin / read & write
everyone / read
*Microsoft autoupdate* _unknown / read & write
admin / read & write
everyone / read
*Microsoft office 2008* system / read & write
admin / read & write
everyone / read
Opera myusername(me) / read & write
admin / read & write
everyone / read
Skype myusername(me) / read & write
(unknown) / read
everyone / read
Unarchiver myusername(me) / read & write
(unknown) / read
everyone / read
VLC myusername(me) / read & write
admin / read
everyone / read
*Yahoo Messenger* myusername(me) / read & write
admin / read
everyone / read
It seems as if the mac does not recognize me (in some cases) when I am logged in.. because why do I have 'custom' access, while in the list of users, I can see myself with "read and write" access.
Also, if you look at one of the codes given by V.K to input into terminal, specifically:
*chmod +a "everyone deny delete" ~/ ~/Desktop ~/Documents ~/Downloads ~/Library ~/Movies ~/Music ~/Pictures ~/Public ~/Sites*
*I don't see "applications" there.. could that have omitted the permissions fix?*
Thanks for your attention.
Message was edited by: fayjon99

I think I may have done something not so smart... because I don't know Terminal very well. I did not know that I had to wait for the prompt:
*Macintosh:~ myusername$*
before entering a new command. Because what I did after I entered the first command:
s*udo chmod -R - N /Applications*
and got the reply:
*chmod: N: No such file or directory*
there was a little grey box directly underneath it. So I put the rest of the commands in (pressing enter after each line, which gave me a little grey box on the next line).
Then after a minute or two I closed terminal, but it asked me if I wanted to close it since there were commands running. So I chose "Cancel" but then the terminal dissapeared!!!
Did I do something stupid?
Anyway, I redid it, but this time waited until the prompt with my username popped up and this is the result:
*Last login: Thu May 8 16:50:05 on ttys000*
*Macintosh:~ myusername$ sudo chmod -R - N /Applications*
*chmod: N: No such file or directory*
*Macintosh:~ myusername$ sudo chmod +a "everyone deny delete" /Applications /Applications/Utilities*
*Macintosh:~ myusername$ sudo chown -R root:admin /Applications*
*Macintosh:~ myusername$ sudo chmod -R g=rw,+X /Applications*
*Macintosh:~ myusername$*
I checked the applications folder afterwards, but nothing has changed in regards to my problem. Do I have to reboot to see changes?

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