Yosemite clean install issues

My mac mini 2011 was upgraded to yosemite recently, and basically grinder to a snail pace halt. I took it to the genius bar - nothing wrong with anything via diagnostics. They advised to save all folders from both hdd's on the mini to an external drive. After that they completed a clean install of yosemite, and instructed me to take it home and copy the folders from both drives back to the drives again.

I couldn't have two systems, library and user folders on the one drive - so renamed the ones from my ext hdd with a numeral 1 (system 1, users 1, library 1) just to enable me to copy them across to the startup disk. These did copy although not without issue (icons showed bar wasn't complete when it was, and there is an X in the top left corner of each folder - looks as though only partially copied but checked they have identical content and Gbs).

Now I need to delete the original System, Users and Library (not applications) folders from the clean install, and rename my copied folders as per the original, so my computer will hopefully function normally. I hope.

However, I am completely unable to remove, modify or change those three folders in any way - not even drag to trash, nor rename them.

So....what do I do??? Thanks in anticipation of a wonderful and simple solution that allows me to cancel my re-visit to the genius bar on tuesday!