Mixed up library

I have been trying to solve multiple individual problems with my library, but I thought instead I would ask for help with the whole shebang. I initially began my library by importing references from Endnote, dropping in a bunch of PDF's from my files and using Quosa to try to update some of my info. Since then, I had to reformat my hard drive and, typical for me, had not made a backup file. When I started over, I redid some of my previous steps, but somehow things don't seem quite the same. Some of my files read as cannot be found, and others are doubled up and disjointed. These are the things I would like to do, but I know not all of them are available. Any help on the best way to coordinate my library cleaning would be greatly appreciated!

Steps I would like to take:
Systematically search library to determine which files are clean (reference info is there, PDF is saved, attached, available and renamed)
Delete file info for PDF's that can no longer be located
Use the internet to locate any PDF files that are not able to be found in one batch
Rename these PDF's using the available parent data in a batch
Search and delete duplicate files, combining all available information and checking any contradicting information (I know this is not yet available)
Sit back, relax and enjoy!

Other things that I am not sure if I can do or not are:
When gathering info from the web, only saving associated files that are PDF's (not individual note files that are sometimes included)
At the end of writing a paper, use the reference list to tag all references used in that document with document title
When searching for a specific reference, only showing the parent file and not the attachments (as they spread each result farther apart from one another).

I am sorry for the combined list of current problems/feature requests, after reading up on as much as I can, I still feel like I don't have a great handle on what Zotero can and can't do and what is currently in the works. I love the software though and I have completed 2 papers and archived my entire PDF library mostly successfully.

Thanks again!
-Nicole
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