CPU Fan stopped working after Samsung EVO 850 installation

[evergreen2016]

I upgraded my SSD drive to a Samsung EVO 850 (m.2 500GB) in my Sony Vaio (SVD13233CXB) and it worked for a few minutes but the laptop suddenly shut off on its own. It turns out that the CPU fan suddenly stopped working and the laptop constantly overheats and shuts down. I bought a replacement fan and installed it but it still won't power on.

NOTE: Tested both CPU Fans outside the laptop with 9V battery and they both powered on. (it's a 4-wire)

Tried cleaning and reapplying new thermal paste also but still overheats. The cpu fan and vent were both clean before all this started and the computer is only three years old.

Any idea what might be causing this? The computer otherwise works except for the overheating and cpu fan issue (a minor note, the SD Card reader also stopped working after the SSD installation). Tried to see if the original SSD would make a difference but the problems remain the same.

I checked and re-checked all connections already so that doesn't seem to be it.

Tried SpeedFan and Open Hardware Monitor but the CPU Fan is not detected in either.

My computer is running Windows 8.1 and the UEFI BIOS shows no options for Hardware Monitoring so I can't even check that (anyone have ideas on how to check if the system recognizes the Fan?)

Tried VAIO Care diagnostic but no problem about the CPU Fan gets detected...

Any idea what might be causing this or what would remedy this problem?
Any help would be greatly appreciated. Thanks.

 

[WyomingKnott]

Silly question. Can you replace the old drive and see if the system now works, or if the problem persists? What was the old drive?

 

[evergreen2016]

Silly question. Can you replace the old drive and see if the system now works, or if the problem persists? What was the old drive?

Tried original SSD, another Samsung but no change. Even tried factory reset of OS but still the same.

 

[WyomingKnott]

Sounds like something got broken on the motherboard. If the _only_ thing affected is the CPU fan you could attach it to another header (at a fixed speed of 100%), but the fact that something else stopped at the same time suggests to me that the most likely answer is motherboard damage. I can't fine it down any better than that.