Due to some issues with 2.2.0.734 (background service repeatedly not starting, and "Unable to enumerate folder error" ) I went back to 2.2.0.651.
I have actually already fixed the "other" space - turns out the E:\ "System Volume Information" (outside the poolpart folder) was 700GB. Somehow all the files had no owner and I was unable to take control via Windows 10, so i just deleted that folder through a Linux live CD.
Now, everything seems like it is working. When I first start drivepool, it still warns me of duplication inconsistencies but I am able to resolve it through the software. I also tried setting duplication to 1x for "System Volume Information" but after my first restart I still received the warning about duplication inconsistencies for that folder. At that point I was out of time, so hopefully my next restart won't have that, but even if it does, it seems DrivePool is able to resolve it without me having to do any more tweaking.
I'm running a scan on all my disks right now just to make sure the file system is still intact from the work I did in Linux, and hopefully I can add the remaining 16TB to my pool later tonight.
Thanks for your help.