Ssd or other component making strange noises

[galraphaellll]

So this is my first time installing a new SSD and it works fine, but after a day or two I started hearing noises and I have heard this noise from my system before installing the SSD, but ONLY when I fired up my pc and never when it was already on, it's hard for me to describe but it's like a car starting its engine and very shortly after there's a "boop" sound, like some component is restarting and like I said before, this all happens when my system is already on and I'm logged into Windows 10 so there's no need for a component to restart, also sometimes something makes a shutdown sound randomly while my system is on.
my SSD and HDD are recognized by windows and are both working great, I did a benchmark on my SSD.
One important thing I have to mention is that I installed my SSD literally on top of my HDD as you can see in the pictures, I did this because unfortunately, my case doesn't have any extra space or drawers/cases for HDD/SSD.
Does it make this noise because the SSD is physically touching my HDD?
My only option is to put the SSD inside this Kingston SSD external adapter and plug it to my pc with a USB which its the last thing I want to do because I heard it reduces speeds, although I'm not sure (it's probably a SATA 2 adapter).
Is There a possibility that another component shuts down without warning and it's not the SSD at all?

MY SYSTEM:
NVIDIA GeForce GTX 1050 Ti
8.0 GB
240 Kingston a400 SSD
seagate 1tb
Intel(R) Core(TM) i5-7400 CPU @ 3.00GHz

Pictures:
Forgive me for my cable management it is my first pc
:/
1)https://plus.google.com/photos/photo/105331790318955858863/6596985886966384514

3)https://plus.google.com/photos/photo/105331790318955858863/6596985671554697058

 

[CountMike]

All of your pictures are 404 (URL not found)
Your SSD is external one, how did you install it inside ?

 

[galraphaellll]

I installed it with 2 SATA cables, one is plugged into the motherboard and to the SSD and the other from the power supply to the SSD.

 

[galraphaellll]

I think the noise is gone, I cleaned my pc and reinstalled a fresh copy of Windows , hope it stays this way