Can Find and Replace use regex searches?
Also can it be used to change formatting?

What I would like to do is bold the greek words in a commentary and leave the other words alone. Is this possible? Or is there a module tool for this?

1. No
2. No
3. No but perhaps it could be done with regex directly on the rtf code if it was consistent.

I may have to look at it with Notepad++

The SQlite Regexer at:
http://www.biblesupport.com/e-sword-downloads/file/7416-sqlite-regexer/
may be useful for hacking the RTF code directly.