Question about Removing Permissions from the System Folder with chmod

Hi
I have a question about the removal of permissions from the System folder (and sub directories and files).
Background
Since installing a new HD, clean install of 10.6, application of updates and moving over backed up user directories I have had several issues with permissions.
I have read several threads on this and using disk warrior and other tools I have been able to fix most of the issues.
The Problem
The issue that remains is a permissions check using Disk Utility keeps reporting
ACL found but not expected on "System".
followed by an extensive list of sub directories and all.
Attempts to repair take hours and the same errors are reported.
Found Solutions
I have read about changing and/or completely removing the ACL from the permissions from the System using two different commands:
sudo chmod -R -N ./System/* ( to remove all ACLs)
or
sudo chmod -R -E ./System/* ( to replace all ACLs )
My Question is ( to the UNIX gurus):
What is the difference between the usage with -E and -R and which is the best approach for a Systems directory and (subordinates)?
Many thanks!!

OK
So I misread on the your instructions about the PW reset, did it, no harm in that. I did also select the options to reset all the permissions for all the accounts and the ACL issues were not resolved. My bad, I forgot to note that.
You do suggest getting and expert opinion but alas these are rather elusive. In most cases the Apple solutions is to do a complete reinstall... I have found that unless you completely wipe a drive and rebuild everything there are often artifacts left behind. Since I have full and redundant back-ups I would rather explore and hack a little instead of a dull old system reinstall. The irony is the system issue I had was it was the result a reinstall and combo update on a new drive. I recognize the risks of entering the realms of the System folders but I am willing to explore knowing full well that I have a path to recovery.
Thanks again for your insights. I come to the forums looking for insights and ideas but not a lecture...

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