Cubase 9 and plugin manager

Hey there Cubies
I just installed C9 (actually upgraded from 8.5) and now I’m in plugin hell.
I was going to recount the whole story but I have decided to skip the inexplicable behavior and just ask a simple question.
How do I get out of this mess? What do I need to do to get everything shipshape?

I have plugins all over the place from previous installations. Some were not blacklisted but just do not show up in plugin manager. But they do show up in my list on the right but grayed out.
Some won’t load from my custom list yet load from the default list??

Some I have updated - NI plugs and Omnisphere. I still had to move Omnishere dll into another dedicated VST Plugin folder I made on my D drive before it would work.
Two of the NI effects plugs worked after update. The other two don’t show up anywhere.

Guitar Rig is gone from my plugin manager. . Absynth is gone also even though I just updated it. I moved a couple of NI synths - FM and Massive - from my 7.5 install into my VST folder on D drive. I had previously done this before so when prompted about the file existing I chose “keep both”. Now those duplicates (FM(2)) work but the newer ones don’t.
My fabfilter only has the one stereo VST3 working. The other couple that used to show up are gone
That’s just the half of the drama which I did say I wasn’t going to spell out so I’ll stop there.

What’s the best practice to sort this out?
Do I need separate VST2/VST3 folders?
Where do I start?
Who has crossed this bridge before?
Thanks chums

Had to reinstall a lot of my plugins.
Mostly all working now but I had to jBridge a couple that worked fine in 8.5.
Seems odd?
Still got stuff all over the place going back to C7 but I’ll call it a day.
All the NI stuff just about returned but the 16/8 out Kontakts don’t appear in Cubase as they used to, neither do the surround Absynth versions. Anyone know why?
Still on Win 7 here BTW
Reaktor is also missing but I never saw that on my system with 8.5 and I never used those Kontakt/Absynth ones anyway.
C9 has blacklisted my UAD plugins but only the 32 bit versions, and also Loopmash! which I’ve never even looked at, so tomorrow I can dive into C9 and get a feel for it.
I must say it seemed pretty stable with all the testing I’ve done tonight and looks pretty good.
Just not having those stupid pop out menus will be worth the upgrade for me.

Cubase 9 isn’t 32-bit compatible.