Locked out of additional internal drives... Help please

Any help would be more then welcomed as I did something stupid and need a bit of help to fix it please.
Had an issue today on my Mac Pro (2.8, Quad 5.1). All was running fine until I went to update a piece of 3rd party software (Fetch). After the download I went to drag new version into my apps folder and was told I didn't have permission to instal the app.
Now to be clear, I've had a bit of an issue with this before as I'm running 2 mac pros in different locations and drag and copy files and folders from here to there on a regular basis via FTP and external drives. I also have all 4 slots filled on both systems with various drives set up for a particular function along with a number of externals. I've set permissions on both systems and all drives to "read and write" for both my accounts to have full access and each time "apply to enclosed items" was selected.
But for some reason, from time to time, I have to authorise the file transfer. Haven't figured out the reason but it's not a huge deal so have left it.
Today was the first time I have had access denied for my home folder when working from same system. Not thinking and while on the phone to someone (this is where I did the stupid part), I opened the info on my boot (startup) drive and decided to add both of my user accounts and change permissions for each in addition to the system, admin and everyone that was already there. This was done while working from it directly and then set options to "apply to enclosed items". Yea, smart I know.
About 20 minutes passed and then it told me that it didn't like any of my system extensions. I was forced to do a restart and got the spinning wheel for about 30 minutes. Had to do a force quit and open in single user. Applejack wouldn't help at all, nothing. Had to then open cd drive through terminal just to get systems disk inside.
Restarted from systems disk and tried a simple disk utility repair. System restarted fine but I noticed that I was then locked out of all of my additional internal drives, iDisk included (padlock shown on all drive icons excluding my Boot/Startup drive). Tried opening info on the various drives with apple i option and "permissions denied" popped up each time.
I then took the step to restore from time machine. Set my restore selection to about 2 hours before I became an idiot. After it was finished I restarted the system hoping that would clear up my mistake but same thing, still locked out of all of my drives aside from boot/startup drive.
All user accounts that I have added to the boot drive are still showing, I have yet to try and remove them... Figured I would ask for help before I messed it up any further. Spoke to apple care and they have advised me to do what I have done so far.
Aside from an erase and instal, what steps should I take from this point? Will removing the added accounts clear up the issue?
Also, any idea as to why I was refused permissions to begin with...?
Thanks in advance and sorry for the book, just wanted to be as clear as possible.

Force iPad into Recovery Mode. Follow step 1 to step 3 very closely.
http://support.apple.com/kb/HT1808

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(10595)

Locked out of additional internal drives... Help please

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