I don't think I really have time to do this properly, but here's a go at it. I should note that this topic came up in one of the news groups last year (I think) and David Salo presented a chart which I commented on. Between the two of us I think we had covered most of the points, and I don't recall them all off the top of my head.

But let's begin with the Edain of the First Age. I'll cite descriptions of them from THE PEOPLES OF MIDDLE-EARTH:

  The Folk of Hador [the Marachians] were ever the greatest in
  numbers of the Atani, and in renown (save only Beren son of
  Barahir descendant of Bëor).  For the most part they were
  tall people, with flaxen or golden hair and blue-grey eyes,
  but there were not a few among them that had dark hair, though
  all were fair-skinned.43...

  ...There were fair-haired men and women aming the Folk of
  Bëor, but most of them had brown hair (going usually
  with brown eyes), and many were less fair in skin, some
  indeed being swarthy.  Men as tall as the Folk of Hador
  were rare among them46, and most were broader and
  more heavy in build.  In association with the Eldar, especially
  with the followers of King Finrod, they became as enhanced in
  arts and manners as the Folk of Hador, but if these surpassed
  them in swiftness of mind and body, in daring and noble
  generosity, the Folk of Bëor were most steadfast in
  endurance of hardship and sorrow, slow to tears or to laughter;
  their fortitude needed no hope to sustain it.  But these
  differences of body and mind became less marked as their
  short generations passed, for the two peoples became much
  mingled by intermarriage and by the disasters of the War.

Note 43 reads:
  No doubt this was due to the mingling with Men of other kind in
  the past; and it was noted that the dark hair ran in families
  that had more skill and interest in crafts and lore.
Note 46 reads:
  Beren the Renowned had hair of a golden brown and grey eyes;
  he was taller than most of his kin, but he was broad-shouldered
  and very strong in his limbs.

These descriptions differ slightly from the descriptions provided at the end of "Of the Coming of Men into the West" in THE SILMARILLION:

  ...The Men of the Three Houses throve and multiplied, but
  greatest among them was the house of Hador Goldenhead, peer of
  Elven-lords.  His people were of great strength and stature,
  ready in mind, bold and steadfast, quick to anger and to
  laughter, might among the Children of Iluvatar in the youth
  of Mankind.  Yellow-haired they were for the most part, and
  blue-eyed; but not so was Turin, whose mother was Morwen of
  the house of Bëor.  The Men of that house were dark or
  brown of hair, with grey eyes; and of all Men they were most
  like to the Noldor and most loved by them; for they were eager
  of mind, cunning-handed, swift in understanding, long in
  memory, and they were moved sooner to pity than to laughter.
  Like to them were the woodland folk of Haleth, but they were
  of lesser stature, and less eager for lore....

Now let's take a look at Tuor as he is described in UNFINISHED TALES in "Of Tuor and his Coming to Gondolin":

  Therefore Rian arose and left the dwelling of the Elves, and
  she passed through the land of Mithrim and came at last to the
  Haudh-en-Ndengin in the waste of Anfauglith, and there she laid
  her down and died.  But the Elves cared for the infant son of
  Huor, and Tuor grew up among them; and he was fair of face,
  and golden-haired after the manner of his father's kin, and
  he became strong and tall and valiant, and being fostered by
  the Elves he had lore and skill no less than the princes of the
  Edain, ere ruin came upon the North.

Now let us look at the description of Aldarion (sixth King of Numenor) from "Aldarion and Erendis" in UNFINISHED TALES:

  The son of Meneldil and Almarian was Anardil, afterwards
  renowned among the Kings of Numenor as Tar-Aldarion.  He had
  two sisters, younger than he: Ailinel and Almiel, of whom the
  elder married Orchaldor, a descendant of the House of Hador,
  son of Hatholdir, whose was close in friendship with Meneldur;
  and the son of Orchaldor and Ailinel was Soronto, who comes
  later into this tale.

  Aldarion, for so he is called in all tales, grew swiftly to a
  man of great stature, strong and vigorous in mind and body,
  golden-haired as his father, ready to mirth and generous, but
  prouder than his father and ever more bent on his own will....

And here is a description of Erendis:

  ...To the feasting in Armenelos came one Beregar from his
  dwelling in the west of the Isle, and with him came Erendis
  his daughter.  There Almarion the Queen observed her beauty, of
  a kind seldom seen in Numenor; for Beregar came of the House of
  Bëor by ancient descent, though not of the royal line of
  Elros, and Erendis was dark-haired and of slender grace, with
  the clear grey eyes of her kin.

I should point out here that Beregar was a descendant of Bereth, the sister of Baregund and Belegund, the two nephews who stayed with Barahir and were killed with him in Dorthonion by the Orcs. So Beregar was literally a descendant of Bëor, and not just a Bëorian, as the text might seem to imply.

Earendil, the son of Tuor and Idril, was golden-haired like his parents, and though Elrond was dark-haired there may be reason to suggest that Elros was lighter haired. His descendants, apparently strong in Marachian blood, appear to have been mostly golden-haired. It is not clear, though, whether Ar-Pharazon was golden-haired. In several places he said to have been "a man of great beauty and stature, in the likeness of the first kings of men", and I infer from that a high probability he was golden-haired.

"Akallabeth" (and other sources) states that the Elf-Friends dwelt mostly in western Numenor near Andunie, one of the two havens where the Eldar most often came to visit the Numenoreans (the other chief Haven was Eldanna, which lay south of Andunie). In a note to "Aldarion and Erendis" (Note 19) Christopher Tolkien points out that most of the people of the westlands were descended of the Bëorians. It is largely on the strength of these two points that I have suggested (in the past) that the Dunedain of Arnor and Gondor were mostly of Bëorian stock, although that is by no means certain.

The Bëorians left their lands (Ladros and other parts of Dorthonion) around the year 455 in the First Age. Most of them passed west to Hithlum and were joined to the Marachians (the Folk of Hador). But it should be noted that there were still many men among them. They did not vanish as a people. A second wave of Bëorians (apparently much smaller than the first) left Dorthonion and went south to Brethil, from whence the majority passed on to Hithlum to join their kin. This second wave was the group led by Emeldir the Man-hearted, wife of Barahir (and she promptly disappeared from history, along with her daughter, Hiril).

The First Age ended about 135 years later (the year 590). In other words, about five generations passed after the Bëorians settled in Hithlum. At least three of those generations were spent in slavery, from the time of the Nirnaeth Arnoediad (472) to at least the beginning of the War of Wrath (547). During that time the Bëorians could have become merged into the Marachians, but Note 19 to "Aldarion and Erendis" indicates they retained their ethnic identity to some extent. So they must have settled in separate communities from the Marachians in Dor-lomin.

As you noted, the Dunedain of THE LORD OF THE RINGS are dark-haired, grey-eyed, and fair-skinned. It appears to me that basically the Faithful were mostly Bëorians, who when they left Numenor tended to settle in the lands around Pelargir or in Eriador. All of the Dunedain who fled the Downfall in Elendil's nine ships were Faifthul, and therefore probably were from western Numenor (since the vast majority of the Faithful came from that region), and thus they, too, were probably largely of Bëorian stock.

Hence, the explanation seems to be that the Black Numenoreans were for the most part descended of Marachians (and/or the Folk of Haleth) and the Faithful were descended mostly from the Bëorians.

I hope that provides the kind of answer you were seeking.

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Parma Endorion: Essays on Middle-earth, Revised Edition