Dear John,
 
Let me start from the very end of your letter:
 
[A]
> That's why I don't think that the Ghassulian culture can represent
> early
Semites.
[J]
And this is why I think they can.  But I am not inflexible on the
topic and can be pursuaded otherwise.

[A]
So am I.
"Early Semites" in my sentence means a group which can be ancestral for _all_ (North)Semitic tribes, including Akkadians, Assyrians, Amorites, Arameans etc.
However, from my point of view, theoretically the Ghassulians could represent a "local" group of people speaking a Semitic language who passed to a sedentary way of life (the Mediterranean one in this case but not Mesopotamian one as in the case of Akkadians).
 
You wrote:
 
The shift two and
fro between sedentary mixed agriculturists --> transhumance
pastoralists --> fully nomadic pastoralists and all the way back
again is one that happened repeatedly for the Semites, I feel.  
  
 
[A]
My feelings are a little different. IMO the ways from sedentary way of life to pastoral nomadism and in the opposite directions are long and painful processes. I don't think that it can happen repeatedly (pendulum-like) in the history of a tribe.
 
In the situation when
(A) we see at a site the transition from nomadism (phase 1) to sedentary life (phase 2), then nomadic pastoralism dominates again (phase 3), and then again we find a sedentary population (phase 4), 
and
(B) we know that language of people of the site remained almost the same,
I would be inclined to interpret it as the following:
 
1. A part of a nomadic population passed from the nomadic way of life to the sedentary one (because climatic conditions favour this), whereas the rest of the population remained nomadic (because the tradition and the Gods of parents were against this) - phases 1 -> 2 ;
2. Climatic conditions changed (got dryer) and the latter group ousted the former one (because the Gods punish renegades) - phase 3 ;
3. The new population of the site still passes to the sedentary way of life (because olives are so fat and grape is so sweet) - phase 4.
 
 
You wrote:
 
From what I have read, it would seem that all the place-names within
the orbit of the Ghassulian culture zone are Semitic in origin. 
There does not seem to be any underlying sub-strata that can be
identified.  If Ghassulian is non Semitic, I would have thought that
traces of this non Semitic sub-stratum would have survived to
Biblical times at least.

[A]
An important fact, indeed. But...
I guess the Ghassulian culture zone is Palestine and perhaps South Syria (please correct me if I'm wrong).
Anyway there lived somebody who didn't belong to Afrasiatic->Semitic linguistic branch - either PPNA or PPNB. If you state that the Semites came from Africa, then neither of them. Thus we have 2 non-Semitic substratum layers, even if we stay aside the Ghassulians. Why none of these substratum layers have survived to the Biblical times? Too long? Yes, however the distance from the Chalcolithic to the Early Iron Age is not very short too. 
I just don't know - what is the longest space of time which _must_ be survived by substrate toponymes for sure? Do such estimations exist?
 
 
Best regards,
 
Alexander