Learn English – Difference between “I went to the toilet” and “I had gone to the toilet”

When talking about things in the past, the past perfect happens before the simple past.

In your example

If someone feels that they had never made a mistake in their life, then it means they had never tried a new thing in their life.

had never made and had never tried are two actions which were started and ended in the past compared with how the person feels (present). The equivalent would be

If someone feels that they never made a mistake in their life, then it means they had never tried a new thing in their life.

where never made is nearer in time than had never tried since one would have had to try before failing.

I had called you
I had gone to the wash room

could individually use the simple past

I called you
I went to the wash room

with similar meaning, however, using past perfect sets up a scenario for something in the more recent past

I had called you before I went to the wash room
I had gone to the wash room before I called you

To answer where you were when they called:

I had gone to the wash room when you called me

means you were in the wash room (past perfect) when the person called

I went to the wash room when you called me

means you heard the phone ring then went (simple past) to the wash room

Please see this post which contains a lot more information on how and when to use the perfect tenses.

To briefly answer your question: As you say, the perfect tense is used to relate two actions or imply a time relationship between now and some action. "When I was younger" is an adverbial phrase, not a separate action. All it does is tell you when something happened, no different from saying "yesterday" or "last year" or "in prehistoric times". Just setting a time frame for an action isn't enough to justify using the perfect tenses -- there has to be a good reason to relate two actions. For example:

When I was younger, I had wanted to be a doctor.

Incorrect. Simple past is sufficient. "I wanted to be a doctor".

When I was younger, I had wanted to be a doctor -- until I saw the movie "Top Gun". Then I wanted to be a fighter pilot.

Correct. "Had wanted" implies it was true, but something happened to affect that desire.

With this information you should understand why "I had gone to the store" is incomplete. You need to have something else happen to justify using the past perfect tense:

I had gone to the store when I remembered I was late for an appointment.

I had just gone to bed when there was a loud noise outside.

I'd started the exam before I discovered I'd forgotten all my pencils at home.

As with most things in English there are subtleties and exceptions with the perfect tenses that you have to learn with practice. Hopefully this will be enough to get you started.