Yes, when AutoCorrect is active in a project it can make trying to type certain characters difficult. I would suggest typing those characters in a different location (maybe a Notepad file) and the copying/pasting them into the find dialog. It is important that punctuation be used consistently, so if you are currently typing the smart single quote rather than >, I would make sure that the replace window is replacing with the correct character.
When you have the punctuation inventory open you should be able to see a concordance view of the issues at the bottom of the window. Double clicking on one of those entries should take you to that verse in the text and highlight the issue. You can then use CTRL+h to open the find/replace dialog to locate the rest of the items. Whatever text is highlighted when you open the find dialog should appear in the find window.
While it is possible to open and edit the text files (in your case .sfc files), I would recommend working within Paratext if at all possible. And make sure you do S/R before and after working on these kinds of changes - since they can affect a number of different verses.