If most of your online tree is other peoples work and imported into your tree, actually multiple trees in the one file. Would it be easier and less time consuming to just delete your entire file, or mess, and re import the desired and best tree that you are happy with??
If a large portion of your file is real research and hard work that you have spent much time and have worked up yourself and then imported others, in duplicates, stuff into the hard work, I guess to try to sort that out and delete the mess.
Good luck with it all and I am impressed that you recognize the mess as a mess and dedicated to getting it right whatever it takes to resurrect, or start all over, your file.. a judgement call for sure.
tick, tick, tick
I did go to your largest family file and the,, "Index A-Z,,,, and did see several dupes on each of several pages of the index so it doesn't appear to be near as bad as most that I see in Public Member Trees.
I'm also glad to see someone as yourself with the pride to clean it up and get it right, so many don't.