It seems evident that no certain solution to the problem of Baja California's linguistic geography is possible, given the inconsistency and imprecision of so many of the early accounts. The best we can do is to try to arrive at a most probable estimate based on the available evidence. In that spirit, here are my thoughts on a couple of the issues you raise in your chapter on the Guaycura language(s ?).
On the issue of whether there was a language distinct from Guaycura that was spoken in the Magdalena Bay area, I think this remains an open question. There are several hints of something of the sort in the sources, but in light of the other inconsistencies in those accounts, I don't think they quite add up to a probability. If there was a distinct language, it might have been related in some way to the Huchití, but I don't think the balance of evidence supports that conclusion. You accept Burrus' identification of Hostell's Huicipoeyes or Huchipoies with the Huchitíes, rather than with Baegert's Utschipujes, which is a possibility, but it seems rather unlikely to me phonetically. A key argument for linking the Huchití to Magdalena Bay in your account seems to be the supposition that the expedition sent south against the Cape rebels might have traveled there, and that Taraval might have been referring to the Magdalena Bay area as the ancestral homeland of the Huchití. I don't see how the passage that's quoted leads to such a conclusion. It seems more consistent to me to suppose that part of the west coast being referred to was the area around Todos Santos, where we know that the rebels had been active; an association of the Huchití with the latter area would be more consistent with other sources.
On the Cubí question, you evidently accept the identification of the Cuvé with the Guaycura, but not the identification of the Cuvé with the Cubí, an equation that seems very likely to me. Although this is just speculation, my guess would be that "Cubí" = "Cuvé" was either the Monqui name for the Guaycura as a whole or else a local term used by some northern Guaycura for themselves. The latter case would put Cubí in the same category (in my view) as the names Huchití, Periúe, Aripe, Callejúe, Vinée, Cantile, etc., used for assorted southern Guaycura groups, or as several "ethnic" labels applied to various Guaycura groups on the Magdalena Plains or at Magdalena Bay by Baegert and others. I don't think any of these necessarily imply a language-level differentiation. I would further speculate that Guillén recruited some northern Guaycura (Cubí) men before the start of his expedition, that they served as packers, guides, and translators throughout the trip (and were sometimes referred to as in his diary as "our friends"), and that Guillén accordingly occasionally lapsed into using the term "Cubí" as a synonym for the better-established ethnic label of "Guaycura", both in his diary and in his later report. This is similar to the way some other early writers seem to have used "Pericú" and "Cora" as fully interchangeable alternative labels, without implying any linguistic or geographical distinction between them. A European analog might be "Deutsche", "Allemand", and "German".
You interpret the comment by Guillén that "they did not know if the people were Guaycuras or Cubíes" as clearly implying that the Guaycura and the Cubí were two different groups, but I don't see this as necessarily so. The word "or" could be contrastive here, as you suggest, but alternatively it could just serve to juxtapose two synonyms (as possibly we might say, "they did not know if the people were Deutsche, or German".) This latter interpretation seems to be supported by the March 14 entry, when Guillén wrote, "hallamos una ranchería de guaycuros o cubíes con solas dos mujeres y algunos muchachos"; in that instance, the travelers would have had an opportunity to determine which group was involved, if a distinction between Guaycura and Cubí rather than an equivalence were being implied by the word "or". If the words were being used as synonyms in the first case, the uncertainty that was being expressed about the identity of the erstwhile inhabitants would concern whether they were (a) Guaycura (or Cubí), or (b) Pericú (or Cora).
Note also that Guillén commented that "Here the territory of the Guaycura, or Cuvé, nation begins", but he never wrote, "Here the territory of the Uchití nation begins" or "Here the territory of the Cubí nation begins". Identifying such limits would certainly have been pertinent to the purposes of his diary, but I think he believed that he was traveling entirely within the territory of a single "nation" up to his arrival at La Paz.
Another way to try to assess the likely degree of linguistic diversity within "Guaycura" territory is to consider the temporal and spatial scales involved. Your account of intermixed language groups seems to suggest that a pattern of ethnic migration was very active in bringing in new groups from the north and scattering them territorially. I certainly agree that ethnic boundaries would not have been completely rigid or impermeable, but the evidence suggests to me that ethnic units in the southernmost parts of Baja California (in marked contrast to the central part) had probably been relatively stable over a long span of time. The Guaycura language, if it's related at all to Cochimí and the other Hokan languages, had evidently stood apart as a separate entity for a minimum of 5,000-6,000 years, and probably longer. Internal differentiation among the Yuman languages of northern Baja California seems to go back some 2,000-3,000 years, so the Guaycura were probably within Baja California at least that long. In the short term, active patterns of migration and interethnic conflict could produce complexity in linguistic geography, but over the longer haul they would tend to eliminate diversity through attrition. The long-term survival of the small Guaycura and Pericú language communities in southernmost Baja California suggests to me considerable territorial stability.
Spatially, language communities are not indefinitely divisible units. For hunter-gatherers, a population of about 500 seems to be the minimum that can maintain permanently a separate linguistic identity, and most groups were probably substantially larger than that. If there had been half a dozen or more different languages spoken within "Guaycura" territory, that would make this area linguistically one of the most diversified parts of aboriginal North America. That isn't what we would otherwise expect for mobile, desert-dwelling hunter-gatherers.
So here's where my views stand, at this point. I think that quite likely there was only a single language spoken throughout Guaycura territory, although there was definitely a significant amount of dialect-level variation. It's possible that were one or two other languages that were fully distinct from Guaycura, either around Magdalena Bay or in the southern area, but I don't believe that the bulk of the evidence supports such a conclusion at this time. Cubí was evidently used by Guillén as a synonym for Guaycura, after perhaps originally being applied to a more limited northern Guaycura group. Huchití was probably originally a name applied to a southern Guaycura social unit and subsequently was extended by some writers either to embrace several southern groups or as a synonym for Guaycura as a whole. Don
I have reviewed the evidence again, and as I said before I don't think we are that far apart especially on the overall picture of considerable linguistic diversity among the various Guaycura bands.
There is certainly no smoking gun, but it is suggestive that the new data about the Cubi confirms rather than disconfirms the amount of diversity involved. Guillen talks about them as if they are not simply the same as the Guaycura of Los Dolores, but somehow alien to them. I don't make too much of Burrus' identifications, but both Hostell and Baegert insist on the linguistic differences on the west coast. And incidentally Baegert put the size of the Ikas at about 500. I also think that Taraval's geographic remarks carry a certain weight because of the distances involved. It is quite a hike from Los Dolores to the Cape Region.
I took another look at Guillén's 1730 Informe, and was struck again by how he juxtaposed the Cubí who were harmful to, or killing, "nuestra gente," making me think that Cubí was not simply a synonym for Guaycura. But all this is sort of like trying to put together the puzzle with not only the picture on the box gone, but most of pieces, as well. Jim