If you’re not using source control, Araxis Merge is a very nice file compare program. You can point it at two directories and it will show you the differences and let you synch them. I used to use it to migrate code back before I began using source control and automating deployments via Jenkins.
Also make sure you check the data in your database. If the extra code being inserted is not in the actual .cfm files, it may be part of values you’re outputting from the database onto the page.
ColdBox Platform Evangelist
Ortus Solutions, Corp