What I found out was that it's possible to waste hours reading crap on the internet and have no better solution at the end of your time. The basic gist of my research is that there is no way to do accurate real-time work on a modern computer and "Guarantee" that it will work flawlessly. Even on a single proc machine let alone a multi-core machine with BIOS problems where cores get out of sync.
This realization scared the crap out of me at first until I realized that there have been hundreds and thousands of games released over the years that had this problem and are fine. The reality is that the world is an imperfect place so why should computer times be any different?
So I'm going to keep using QPC and just set the thread affinity like I said in the first place to take care of the multi-core problem. Outside of that you're all on your own!