I added the 'u' to the cp command as I had to run the script twice. The first time I had errors with '&' in file names, so added the extra line to change them to '/&'. The second time ran through perfectly, user permissions etc were all fine.
I've just checked the log file again, and it does have lots of entries with /../. Actually because that client is an outpost of a Korean multinational, most of the file names and paths are full of strange characters (the console not able to display Korean!). All went back into their correct places though.
When I ran the script on the second machine (which was English), the sript ran without errors.
I can only suggest that there are other 'characters' than need delimiting like the '&' I found. Once you find what the offending character is just add an extra line the change it to '\&\ etc.
I'm running the script on the other two known machines later today (being morning now in Sydney).
Let us know how you get on, 113,000 files should turn up a few more issues. Good luck.
Craig