Find all pages where used JS files

Unfortunately there is no direct way to find out this in one go.

However, open the Fiddler and send SharePoint requests from browser to see the custom files getting loaded. 

I have no knowledge of Sharepoint. However, when you say SharePoint pages, I believe you mean .aspx pages, right?

 

If yes, you can always use something like NotePad++ and use feature like 'Find in Files' and give a search string like '.js' and hopefully you will get all references. Keep 'search in sub-folders' checked.

 

If you have a more specific word to search for, better.

 

Hope it helps!