Here is what I would do (since you have multiple machines). This may only work too for some of the audits that you have listed.
I am not sure if your familiar with the free cleaning tool called CCleaner? I have found the following to be useful for me.
1. Download, install, and configure the program CCleaner (talked about in the following post: http://forums.eeye.com/forums/t/752.aspx )
2. Download the un-installer tool for Flash Player from Adobe's website: http://kb2.adobe.com/cps/141/tn_14157.html OR a direct link to the executable used for Windows from that page is: http://download.macromedia.com/pub/flashplayer/current/uninstall_flash_player.exe
3. Download the latest version of Adobe Acrobat Reader from: http://get.adobe.com/reader/?promoid=BUIGO
3. Take a blank CDR disc and burn to it the entire "CCleaner" file folder (from under Program Files on your system), the flash player un-installer file, and the Adobe Acrobat Reader installation package file.
NOTE: Make sure you configure CCleaner completely the way you want it before you burn it to the CDR, thus your preferences will stay the same on the disk.
Take this disc you have created to each machine that you are having issues with.
4. First run the Flash Player un-installer tool to remove any traces of Flash Player.
5. Un-install Adobe Acrobat (if it is currently on these systems you talked about) either through windows or the un-install function built into CCleaner.
6. Restart the computer system
7. Now, run the "Cleaner" function on the left side of CCleaner's sidebar
8. Run the "Registry" function on the left side of CCleaner's sidebar (be sure to keep running this until nothing shows up in the window).
9. After running these cleaning options, restart your system and then re-install Adobe Acrobat (update it too) and then Flash Player.
Hopefully this will help you clear up two of your audits.
I recommended the CCleaner tool on a CDR because it is nice to be able to take to multiple computers, run it, and cleanse each one of these systems without having to install the program on each system. I have found that it cleans a lot of the junk in your registry that sometimes gets hit on my Retina.
The remaining audits, eEye will have to provide advice on, because I am not sure exactly what Retina is looking for when it hits on those particular audits.