I don't think so. OS X puts its fonts in /Library and System/Library. /user/Library/Fonts is normally empty until the user adds applications or his own fonts.
I did have some in the 'user' folder and restored those to be safe. Not sure when they were added though. In the 'system' fonts folder, I am guessing that nothing was touched here based on my Time Machine folder comparison so I've let it be.
and on a related note, there was an option in the custom settings of the MS Mac Office installation to install 'fonts' (or was it 'additional fonts' ?) that, in hindsight, maybe i should have unchecked.
I don't know about that. Office fonts can only affect how Safari and sometimes other apps display Arabic. They can't damage Geeza Pro or other Mac fonts that should normally be used to display Arabic. I don't know of any way they can affect how your Arabic emails are displayed on the recipients machine.
I don't know either but what I can tell you is that, as far as my experience goes, the email issues have been fixed. It was a very strange issue in that only emails that were started in Arabic on another (windows in my case) machine and sent to me and then replied to in Arabic would experience this. I will continue to observe and report any issues experienced for the benefit of others who may come across the same.
BTW - is there no simple standalone fully-compatible MS Office viewer for Mac? Quicklook doesn't do it too well and I am getting tired of having Mac Word for this purpose only.