The upgrade/downgrade would be most likely guaranteed to corrupt any security software. But now that you are back to factory you need to update the system big time.
Make sure everything is updated, including any parts you may not use (Internet Explorer for instance is important for other processes to work in the background but does not have to be your default browser).
Uninstall all McAfee via Control Panel > Programs and Features, reboot.
Doiwnload a fresh copy of the MCPR cleanup tool again and run it, reboot. Even if it fails it should be run, if it wont run at all then call Technical Support link below, it's free.
Reinstall McAfee from your online account and if necessary, use the Custom option to only install the parts you want.
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If I may add to Colleague Ex_Brit's excellent suggestions. Although you seem to be 'Computer Savy' if you will. I would avoid 'Registry Cleaners' at all costs. For eventually they cause more harm/issues to your system's performance, than good.
Although 'CCleaner' is indeed one of the more trusted ones on the Market. (I have even used it a couple of times myself) one has to be extra pre-cautious especially when using the 'Registry' Feature. It can possibly remove vital system processes, to include McAfee Core processes.
Even when I use McAfee Quick Clean, I avoid using the 'Registry Option'. Your Windows built-in utility 'Disk Clean' should suffice and is much safer. Also when performing a major upgrade it is best to at the minimum, disable your Anti-Virus or even better Un-install it to prevent any complications during the Installation process.
As a ' Side Note ' I would like to welcome you to the McAfee Communities. For your 'Username' looked familiar. After checking my list, I was the Moderator whom 'Approved' your Membership Request. Should you feel you need further assistance, either myself or one of my Colleague's will oblige.
Wishing you all the very Best,
McAfee Community Moderator
Hi There. Sorry for the late reply been a bit busy I fully updated the pc and did another install and it now works fine. However the tool did not work thanks to your patience. Vipercar