Learn English – Using ‘Present Perfect’ with ‘in the past’

Let's look at a little more context:

When the night has come and the land is dark
And the moon is the only light we see
No, I won't be afraid, oh, I won't be afraid
Just as long as you stand, stand by me

A perfect construction marks a past action as having brought about a state which is relevant at some later point: the utterance’s ‘Reference time’.

In the utterance at hand, that Reference time is defined by the main clause—I won’t be afraid—as some sort of ‘future’. (It may be an actual temporal future, or a ‘consequential’ future; that doesn’t really matter.) This future is expressed using the present tense of will, so the state of night and darkness is expressed using present constructions: The night has come, the land is dark, the moon is the only light.

The perfect construction is employed in the first phrase to signify that night is not in the process of falling: it is not dusk, when light is fading, but already full night, when the light is gone. The state of night is fully realized.

When everything is dark I will not be afraid.

Adverb placement is not fixed, and as with other elements, I think most of it depends on what you want to express.

"He has always been an academic and a charitable person". This is a kind assessment of a man, and also the simplest and most common construction.

"He always has been an academic and a charitable person.* This is more emphatic, as if in defense of some alternate version of his history.

"He has been a wise and, always, a charitable person." This emphasizes the constancy of the latter attribute. All are "correct".

"We had been slowly drifting down the river when a bear attacked." is no different really than "We had been drifting slowly down the river when a bear attacked." To my ear (AmE), the latter sounds a bit more common. I agree it would be unusual to break up had been in this case, but "he had often been seen..." is not an unusual construction.

"He had been either sick or exhausted." is much the same as "He had either been sick or exhausted." Here, either is emphasized because of it's less common placement. Both are grammatically correct.