This is too much to read so maybe I'm giving moot advice. NI is not super flexible about moving things around after installing them and sorting out problems once they arise is, imo, not worth the time.
Best thing to do is just re-install everything fresh. Their Native Access installer makes this easy. If you have the space on your C: drive, just leave the default folder settings, but note what they are during the installation. Then all you need to do is point Reaper to that same location by adding the path in preferences>plug-in>VST in preferences and the plugins should appear.
If it does not appear, you need to clear cache and re-scan in that same part of preferences.
I also had a lot of headaches starting out with Maschine, but it's really awesome once you get established and many of the problems I had have been fixed since then. So be patient and then enjoy!
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