Things missing upon re-installing AE

Hello All,
Mocha4AE kept crashing. After trouble shooting, Imagineer Systems said the solution was to re-install AE.  This did allow for a working Mocha but now other things are missing. 
I had intially installed CS5.5 production premium from the web.  I also had physical CDs mailed to me for back up.  I uninstalled AE and re-installed it from the back up CD.  Before uninstalling I moved my Scripts folder, Plugins folder, Presets folder, and CS5.5 folder that is located in the Library>Adobe>Common>MediaCore to a safe location so that I would not loose any of the third party items that I had purchased.
After the installation I put the newly generated Plugins, Scripts, Presets and MediaCore folders in the trash and replaced them with my old ones, which have all of my third party stuff.  Was this ok to do as now I am getting the following warnings, or could the missing things be because they were not in the Back Up CD.
These are the 3 warnings that I get when I start Up AE.
Thank you in advance
on a Mac  CS5.5  OS 10.6.8   12mb ram

Running the Cleaner Tool seems to have solved all the problems.  The only gripe I have is that the instructions are not as clear as they should be.  The product that I wanted to clean and re-install was specifically AE. 
I backed up my AE scripts, presets and plugins, and I though that since I uninstalled AE, as instructed, the cleaner was going to clean only any AE leftovers, but it cleaned Pre Pro, Audition, Photoshop, Illustrator and several other Adobe CS programs completely off my hard drive.  Luckily I didn't have any third party plugins for those items or they would have be lost.
Also Adobe needs to make a list of what folders should be backed up and where they are located for each of their products. I'm sure this would save countless customers from headaches.  A good title for it would be "THE BACKUP BOOK, where your custom content is stored."
thanks

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