No, sorry. I try to keep everything intuitive and give description instructions otherwise. If you have any specific questions, ask away. The worst part is probably creating and assigning prefixes to forums (etc).
I don't understand what you mean.
I can't tell from your description. There could be other search constraints (a particular app or forum) that is preventing it from returning other results. Or maybe it's an outdated cache/search index.
Again, sorry, I don't understand the question.
Please go in FTP to uploads/logs/ to find your error logs, download 2015_11_29.php, and PM it to me. That should tell me what the actual error is.
Do those results that don't have the prefix anymore still have it as a tag? IPB won't let you search for a prefix specifically, just a generic tag/prefix search. So any that don't have it as a prefix probably still have it as a tag. Depending on how you changed the prefix, if they are still there as tags, that may or may not be a bug. Otherwise, if no tags, could be an outdated tag cache--try recaching from this app's tools.