I want to only scan user files and folders - what's best method(s)?

I am involved in a project where dozens of office computers at 20 different locations are to be 'certified' as spyware / malware free. My team will only be backing up, scanning then restoring user files and folders. Another team will 'flatten and rebuild' new machines with fresh OS install and application and protection software. My team will restore 'certified clean' user data onto newly rebuilt systems.

Please tell me, can my proposed approach here be improved upon?

Mostly for accuracy of disinfecting, not so much for efficiency (cannot compromise level of assurance of sanitization for sake of efficiency).

My proposed approach per computer:
1. Remove HD and place into external USB disk enclosure
2. Attach USB enclosure to my laptop, mount and take snapshot image (for backup and later analysis, will use Acronis or Macrium backup tools)
3. Scan entire USB attached disk with Superantispyware and save log file with backup image for later analysis
4. Copy only user data folders and files to a separate USB hard drive for a couple of reasons. A) To separate it from OS and Programs on original HD and to make it easier to inventory and keep track of, I don't think it will make it safer because original HD should be inert by nature of its OS is not active. B) Also I can now detach the USB HD that has the whole HD from the suspect computer (all these computers will be suspect until 'certified') just to be uber safe!
5. Scan user data folders and files with Superantispyware. Save log. Clean any threats found.
6. Scan user data folders and files with MalwareBytes. Save log, clean any threats found.
6. Scan user data with McAffee (reason for this choice is it will likely be the anti-malware tool installed on the new systems, so I want to make sure user files will for sure be agreeable to this software!) Repair any threats and save logs.
7. Restore user folders and files to (newly installed OS and re-built) user systems.

Questions I have:
> I know most anti-malware creates logs mainly of files that have been found to be infected / bogus. Is there a scanner that will list ALL files that have been checked and state that they were found to be safe?

Thanks for looking this over and especially if you have any suggestions!

 

Oh, forgot to ask, how does one go about scanning PST files to certify they are malware free (attachments and so forth)?

Can PST files be scanned without be 'open' by Outlook or whatever mail they are hooked to? Is there some great utility that will go through PSTs, check and clean them, while writing output to a new PST?