Performance Decrease after Factory Reset

Recently my SSD that my OS was located on became too full, and I decided to do a factory reset of my computer. Before the reset my BIOS time was always less than 10 seconds, and averaged around 5. After this reset however, my BIOS is 105 seconds, my frames have begun to drop randomly when playing games, and when I attempt to shut down my computer, the screen powers down but the computer takes over an hour to fully shut off.

My computer is an Alienware 17 Laptop
i7 6700HQ @ 2.60 GHz
16 GB 2133 mHz RAM (I don't know if it's DDR3 or DDR4)
Intel Integrated Graphics 1 GB
NVIDIA 970M 2GB
SSD is 128GB with OS
HDD is 1TB

You might have to get a bigger SSD or delete some stuff or migrate some data to your HDD

After the reset, my SSD is over 75% empty and has more than enough space.

Go to

CrystalDiskInfo Crystal Dew World

Download crystal disk and see if your SSD has some bad sectors or if its going bad.

I used the CrystalDisk tool on my SSD, and it says the health is good. The only problem was temperature, but I've been running tests and diagnostics.

After the BIOS is done, it takes around 30-40 more seconds to be able to log in. I think there was some setting in place when I bought the laptop from Alienware that got changed, but I can't figure out what it is for the life of me.

If its hanging in the bios its either a wrong setting or its stuggling finding the HD have you checked the second hd by default it may heve been set in the bios to raid. As a quick test un plug the second hd and see if its ok then