So an update, I did what Geek-9pm suggested. Over this weekend, MicroCenter had a really good sale on Crucial SSD's so I grab one, put it in my rig, took out the other SSD and HDD and ran a clean install of Windows 8.1 using an ISO via USB drive. 8.1 was able to install successfully, so I reformatted the new hard drive and left it blank. Re-inserted the old SSD with Windows 8 and the Data HDD back into my rig, and this time I ran an Upgrade via the ISO from the USB....and some how it still FAILED.....
Even though a majority of my programs are on my HDD and Windows 8 is located on my old SSD. I really don't want to do a clean install of Windows 8.1 on my old SSD, because it is my understanding that my programs will still need to reinstalled which will be a pain. Any suggestions?