Hi Limerick,
1) Sure every Mod can change the prefix if necessary
2) That just doesn't make any sense

I'm afraid, you can deactivate the prefixes per forum, but not per usergroup
3) before
and finally:
in fact I don't think this is very easy, according to the changes you've made there will be differnet sets of prefixes for every forum.
You can filter searchresults by prefix, but you'll have to have a searchterm too.
To just find every thread just with a prefix would be a sql query with a huge result if not filtered by forum or searchterm or user or...
If you want to find threads with a prefix from admin control panel maybe my small add-on will help (see first-post)
but for users.... that one's useless
'sid