IF this is not suited to just starting over as USAFRet has advised (very good advice!), there is another process if you have the Windows Install disk (or mem stick), Place your Install disk (if that's what you have) in the optical drive. Now shut down and disconnect all the extra drives, leaving only the SSD and the optical drive unit connected. Boot directly into BIOS Setup and go to where you set the Boot Priority. Set that to boot first from whatever device has the Windows Install stuff on it, and then the SSD second. SAVE and EXIT and it will reboot from the Install device to give you the opening screens of that process. Ensure that it has chosen the SSD as the place to do the Install, and then DO NOT do a normal Install! Instead look though the menu choices for a Repair Install, and to that. This will search your system and find that the semi-hidden files it wants (currently on that 3 TB unit) are missing, and then will place new copies of them on the SSD. From now on it will stop looking for those on other drives and be able to boot with ONLY the SSD attached. Now back out, remove the disk from the Optical drive (if it was there) and shut down.
Re-connect all your other drives, then boot back into BIOS Setup. Re-adjust your Boot Priority to what you want regularly, and SAVE and EXIT to reboot.
Now you have the problem of getting rid of those hidden files on that particular 3 TB unit that is giving trouble. FIRST problem is deciding whether that drive contains any stuff you need. If it does, make SURE you copy all of it to some other temporary safe place, because the next step will destroy everything on that drive.
Once you are comfortable with wiping that drive clean, use Disk Management on THAT DRIVE ONLY! to Delete any and all Partitions it contains, so that it is all Unallocated Space. Now you can Create a New Simple Volume on it, making sure this time to use the GPT Partitioning system. When done, back out of there and reboot to ensure that Windows can access all the drives properly. Now, IF you saved stuff you want back on that 3 TB unit, copy it back to there.