The first sentence, "It had been almost one year since i had seen her" is correct, but only if you are talking about a past event. So if you were telling someone a story about the past.
The second sentence, "It's been almost one year since i had seen her" is not correct because "had" is past tense. If you're speaking you could say "It's been almost one year since I've seen her" where the "I've" is "I" + "have". You would use this sentence if you were telling someone right now that you hadn't seen that person for a year(and may or may not have seen them recently).
The third sentence, "It's been a year for him to go back to his country since he had left his country" isn't correct. Here are a couple sentences you could use instead:
"It's taken a year for him to go back to his country."
When you say, "go back to his country" you already know the person left their country, so the second part of the sentence sounds a little weird when you say, "since he had left his country". You should use one or the other. This sentence means the person is back in their country.
"It's been a year since he had left his country." This means the person could be back in their country, or they could still be somewhere else.
The thing with "has/had/have" + "been" is you are not sure if an event is still happening. If you say "go back" the person has to have already returned, so it's not still happening.
Good luck with English! I hope I have explained this well.