It is interesting to compare this with a similar sentence that does not use the past perfect continuous, but just uses the past continuous:

This is grammatically correct. The grammar is simpler and therefore easier and quicker to use. If the story is told in a linear fashion, there is no need to make the extra effort to construct the Past Perfect Continuous as the meaning is clear. However, if the sentences were switched around, the meaning would be lost:

• I suddenly felt exhausted. I was running for two hours. (The meaning is lost.)

This would not be the case with the past perfect continuous sentence, which keeps its meaning, regardless of which way around the clauses are used:

• I suddenly felt exhausted. I had been running for two hours.

The grammar here shows that the running was in the earlier past (Past Perfect construction) and there is no confusion regarding the order of events.