I don't know whether this'll help much, but here's a shot of my Waves folders and settings.
You'll see the folder is in Program Files x86, even though there are 64bit plugins in there. I doubt that wlc.exe (the licensing centre) would run properly if it was installed in Program Files.
Also I've given myself full permission on this folder.
My remaining x86 only plugin is in the WavesV8 folder.
This has kept the waveshells completely separate.
For backwards compatability with older projects saved with earlier plugins I installed both the x86 and x64 versions. When loading an old project Reaper knows which is which, and loads the V9 x86 versions bridged. So I save their settings as a preset, then replace them with the newer versions.
I hope some of this is of some use.
Steve