Is it correct to say that has, have, had sentences can be changed to has got, have got, had got sentences and vice versa?
Eg:
I have a pencil = I have got a pencil
I had got 2 pencils = I had 2 pencils.
These are right:
I have a pencil = I have got a pencil
I had 2 pencils.
“I had got a pencil” does not mean “I had a pencil”, it means that you had come into possession of a pencil (somebody had given you a pencil).
I think we don’t use “have got” in the past tense, so we can’t say “I had got 2 pencils”, in stead you can use “had”: “I had two pencils”
That’s not true
Please, read my comment above
The British say “I had got”
Americans say “I had gotten”
They are prefectly normal phrases, if put in a proper context.
You can indeed say “had got,” but it will make it sound just as Tort said.
Both are possible in American English.
I had gotten two pencils. - This most likely means you have actively sought and acquired or just received them.
I had got two pencils. - If this were present perfect, “got” would mean you just had them in your possession. Almost nobody would bother with the past perfect in this case, so I tend to think it will be interpreted as “I actively sought and acquired two pencils.”
The first sentence sounds better without “got.”
But I’m talking about the past tense, not the past perfect. So “I had got 2 pencils” cannot be equal to “I had 2 pencils”.
Waiting for your prompt reply 
“Had got” is the past perfect, my friend.
Past perfect = had + past participle.
Had got
Had run
Had talked
Had bought
Had cut
Had made
If you re-read my post, you will see that I don’t find them equivalent.
However, with the present perfect, these two ideas can be:
Does anybody have a pen? I have a pen.
Does anybody have a pen? I have got a pen.
The difference is that almost nobody would express the idea of simple possession in such a sentence with the past perfect, so I tend to think the use of it would almost always be interpreted differently.