TL;DR - Backed up the flash drive, reimaged it and copied as many files over as I thought I needed. Tower booted right up with the web interface but had a stale config. Used SMART report from my diagnostics log to assign devices and then had to re-enter my settings and reload the dockers. Appears to be working now with data and docker settings intact.
Details:
I actually went ahead and copied the flash to my desktop PC and reimaged the flash drive. I copied over as many config files as I could over last night but not the whole folder. I copied the key, shares config files and things like that. I didn't want to just copy EVERYTHING over since there was a chance something was corrupt. But one that was strange is that the disk.cfg (?, I think this was the name of the file) showed the serial numbers of the cache, but not the data disks. When the tower booted, the web interface came right up but I had a stale config. Luckily, I had pulled the diagnostics for this post and it had a SMART report which explicitly listed the serial numbers, sda/b/c/d/e names and the parity/disk1/etc for each of my drives. Using this, I was able to assign the appropriate drives back to their appropriate locations. If not for this, I wouldn't have attempted it since the parity drive is completely overwritten.
Lastly, my dockers were kinda there, but not really. They were all listed, but the icon was a question mark and I got some error about the file wasn't found. So I went and reinstalled CA and manually loaded them all back and it all came back just as it should. I also had to reinstall all my plugins, but that's not a huge deal. Overall, I think I'm in fairly good shape. Now if I can just get things to stay running.... It just seems like a different issue keeps popping up every time I look. lol