Having read numerous posts about this I ended up taking my Late 2011 MBP to Apple genius bar. They ran a test and discovered there was a software issue that was causing my MBP to run slow, and frustratingly it was intermittent, but too annoying.
They ended up scrubbing the hard drive and reinstalling Yosemite and it is like I HAVE A NEW COMPUTER!
Unfortunately I did not do a great job of backing up and alas I lost some home movie files which I thought were kept in iTunes. Key lessons learned.
1. If you have a problem go to Apple
2. Make sure you back up everything.
3. The guy at Apple reckons Clean My Mac might have cause the problem. (Who knows) But I am know reluctant to use it again.