PsyCl0ne

Alright I got it sorted.
 
I dont have proof of exactly what the issue was but by doing the following I was able to get everything working.
 
1) As per Fix Common Problems, I went into each share, deleted the last number for "Minimum free space" put that number back and applied the change.
2) The drives that I am removing from my system since they are listed under "Unassigned Devices" I had to mount all of them and I deleted the only file that I could see which was "data" after once again checking that there were no files in them. To do this I used File Manager in the unraid GUI.
3) I unmounted the drives and stopped the array.
4) Navigating into Settings > Global Share Settings I was now able to see all the drives I am keeping listed in the drop-down menu for "Included disk(s)". I enabled them all and applied. Then I hit the Done button.
5) Started the array back up and I got one more notification from Fix Common Problems for the ISOS share. I repeated step 1 to correct that issue.
6) Confirmed that all the missing directories were now visible under /mnt/user/.
7) Stopped the array once again, went back into the Global Share Settings, deselected all the drives from the inclusion list so that it showed all. Applied the change and then hit the Done button.
8)) Started the array once more and going into every share settings I can finally see all of my array drives in the Inclusion and Exclusion drop-down menus.
9) Quick skim through my data directory, it appears to now have what I would normally have expected prior to this mess.
 
 

Thank you both, I don't have much experience with server hardware and didn't know that there was an option within the HBA to enable drives to boot from but it is sorted now!
 
If anyone else does come across this issue, I have the following hardware: SAS9211-8i + SAS9207-8e.
 
Info for the boot settings was found from https://support.osnexus.com/hc/en-us/articles/212131146-Setting-LSI-SAS-HBA-boot-support