Forms (1) and (2) are fully grammatically valid. Form (3) would in general be used only if a further statement referred to a subsequent event. Most often this would be in the same sentence. For example:
He had been playing for two hours when the lights went out.
But the other event could be mentioned in an adjacent or near-by sentence. For example:
The lights went out while he was playing a computer game. He had been playing for two hours.
In the absence of any mention of such a subsequent event, this use of a past perfect continuous construction would be at best unusual, and arguably simply wrong.
There are cases where a past perfect continuous construction is used but a later event is only implied, or perhaps not mentioned. But they are not the usual case for this construction. A comment mentions the example of:
John was tired. He had had been playing for two hours.
but in that case, an event of John becoming tired seems to be at least implied to occur after he was playing, or after he started playing.