We use the Past Perfect Simple to indicate that a completed action happened earlier than something else.

-By the time I was 15, my father had taught me how to drive a car.
-When you arrived, I had already finished my meal.

We  use the Past Perfect Continuous in the  sentence when the action was not completed

-Jane had been browsing the Internet for about fifteen minutes when she suddenly noticed it was completely dark outside.

 I have eaten the cake <---RECENTLY

I had eaten the cake <--- LONG TIME AGO.

I have been waiting for you for 3 years. <--- RECENTLY you told him

I had been waiting for you for 3 years <---  LONG TIME AGO you told him. and you tell him once more.

Past Continuous = recently ( not too long ago )
Past Perfect Continuous = tells "time"

If you want  use past perfect continuous, just think  " if you want to state "time/duration" , USE IT " 

All the sentences with "have" are present perfect not past perfect.

The last one is past perfect progressive.I can easily explain this to you if you would like a lesson with me.It is hard to explain it in writing,I need to show you examples and have you practise it,if you want ot understand it well.

Basically, Past perfect is used for the "past of the past" , when two actions happened one after the other.
THe present perfect (have +V3) is used to show something in the past which has a connection or relevance to the present, for example "I have finished my homework" or "I have lost my key".

Past perfect progressive is when the first action in the past is a long,continued one.