Permissions issue after Mavericks upgrade

I have just updated an early 2008 IMac with OSX Mavericks.
All software running fine, but I noticed occassionally I was getting an authentication prompt on some files, didn't follow, but simply authenticated as and when I need to, I assumed it was when I moved files from my Mac Pro to my Imac.
Having run the upgrade however, I get an error message to contact the vendor (Battlefront) as my copy of Combat Mission Battle for Normandy has lost its license.
After the upgrade I had also purchased from the same vendor Combat Mission Fortress Italy. Having downloaded this and gone to run after copying to applications, this software gives me an error message saying unknown developer so I have got no where near installing a license.
Having contacted the vendor and tried to get a work around, I am now getting the message it is you Mac not our software, despite the fact that all my other software is working fine (and the fact that the Combat Mission Battle for Normandy game worked fine until the upgrade).
I do feel some sympathy for them, I do think the Mac has some sort of permission issue - I also probably compounded this by deleting a user which I did not recognise called 'wheel' which I suspect now is some form of default permisison.
Anyone got any ideas, how do I 'reset' the system - I have tried fixing the permissions through disk utility.
My vendor got me to run a sudo command through Terminal, but I got the message...
sudo: unable to stat /etc/sudoers: Permission denied
sudo: no valid sudoers sources found, quitting

Update Saturday Jan 4, 2014
Before my Mavericks upgrade on my Mac Pro, no problems ever (use my Mac 4-8 hours a day) using my Bose Companion 5 USB connected speakers. I've tried shutting the Mac down and plugging the Bose USB cable into another open USB port = no joy and other combinations. I tested the same Bose Companion 5 USB speakers on two other laptops with NO issues (ouch...they were running Windows 7) I have deleted the two .plist files, did the CMD+OPT+P+R reset, etc... = no change. Looked into Midi Audio Setup and did not see anything in there to change even though I tried a couple of things and no avail (there was no Garageband setting/entry).
I still get a solid "BEEEEEEEEP" sound every 20+ seconds, when the sounds tries to toggle, by itself, between the Bose USB Audio device and the Internal Speakers.

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