I have Waves installed in Win7 x64 with 32b & 64b plugins.
I know some of had installation issues but since I never have & don't know what the cause is I'll just mention my folder setup so you can compare.
I have the typical setup; x64 vst plugin folder in 'Program Files' & the x86 vst plugin folder in 'Programs Files(86)'.
I have a separate 'waves' folder in the 'Program Files (86)' where the Waves Shell-VST9.2.dll is installed.
You don't need to remove older versions but with your issues I'd do a remove/install. Make sure you make copies of your user presets xps files.
I use the WOLI online installer which works well for me.
I can remove & re-install the entire Mercury bundle while I'm having breakfast or taking a break. Individual plugins should take a about a minute or two depending on the size, reverb ir's ect. take longer.