Lightroom :: Installation Of 4.4 Removed Watermarks / Plugins And Non-Adobe Filters?

Asus motherboard, i7, 930.  24 gig Kingston HyperX ram.  Windows 7 Professional 64 bit.  5 SATA hard drives: 3 are WD 7200s;  Driive C is a Plextor SSD and Drive G (where LR and Photoshop are installed), is an Intel SSD.
 
I've had LR 3 and 4 and 4.1,  4.2 and 4.3.  I have several hard drives.  All the LR programs are installed on my G drive.
 
This time when I installed the update to 4.4, it did install on the G drive, but instead of creating a folder in Program Files, all the files, including the executables, simply installed in a long long row under Program Files and under the folders for the previous versions of LR.  It did indeed install 4.4, but it's a mess and I can't figure out why there was no folder created.
 
When going into LR my copyright is gone and all the various styles of copyright I'd created in the Watermarks folder are unavailable.  I also have 2 Nik Filters and 2 Topaz filters - they too are unavailable from the upgrade to 4.4.  I also had a plugin for Zenfolio which is also missing and I can't find any plugin folder.  Where is the plugin folder supposed to be?
 
It has never been clear to me which folders are supposed to reside on the same disk as the main LR program and which folders can be kept on another drive.  Perhaps this is part of why I lost so much information.
 
I do have backups and I've been able to retrieve a lot - but I would like to be able to  have the correct folders in the correct directories and drives.  For example, when I updated to the new camera raw and dng, it was installed on my drive C, as it usually is.  But the LR 4.4 files installed in a big list, although fortunately on the correct drive.  And I have to reset all my settings, all my watermarks, my plugins and my filters.
 
Why did this happen and what can I do to repair it properly both for the best functioning of LR 4.4 and to not have this repeat itself with the next upgrade.