Before moving on to the letter-to-letter transitions, it is worth to study the words by themselves, so that the collected statistics will make more sense.
We don’t know if the Beanish script is alphabetic, syllabic or even logographics, but it clearly looks an alphabetic one. Being alphabetic, it is important to figure out (or at least try to guess) the vowels and the consonants in the alphabet, preferably explaining what the diacritics do. We can make some educated guesses based on the words we have and on the frequencies we have calculated.
In the first sentence, we have a word Ub which like is “are (you pl.)” — the most probable translation is “Who are you?”, but expressed in a language that does not have, does not use or, more likely, does not force the expression of a subject pronoun because it can be derived by other linguistic informations (usually the verb conjugation, such as in most Romance languages). While the phonology of Beanish might allow complex syllable structures such as CC, we should start by the assumption that it favors one of the common CV or VC structures. In Beanish, [b] is far more common than [U] but not that common; a safe assumption is that [b] is one of less frequent vowels (perhaps /u/) and [U] a normal consonant such as /f/. However, we also find [U] as a single word, with no diacritics; we might need to either change the syllable structure to CV or to assign to [U] a “more syllabic” consonant such as “m” (they hypothesis that every letter is a consonant with an implicit vowel seems unlikely by now).
Another short word is 7X. Using the same reasoning,  is likely a vowel such as /i/, and [X] a somewhat more common consonant such as /d/ (I am using English letter frequencies). This would strenght the hypothesis that the most common syllable structure is VC.
In fact, the next short word we have is 4M, and the frequencies would let us assume that  is a common vowel, such as /a/, and [M] a consonant as frequent as [U], perhaps /p/.
Going on, we have the strange [dG] word. Both [d] and [G] are very uncommon, and if the supposed VC structure is used, [d] would be a very uncommon vowel.
It would be easier if we knew about the origin of Beanish. If Beanish is a conlang ex novo, like Esperanto or, much worse, Klingon, we cannot infer much. But I think that Randall has probably derived it from “true”, natural languages. While we could exclude no language, the obvious candidates for proto-Beanish would be languages spoken in France, or perhaps some geographically close language as Catalan — and he might have given us a clue. When reading the comic, I found it strange that the leader of a society as advanced as the Beanish wouldn’t know large numbers when she, in fact, is pretty proficient in English (just don’t blame her for such a strong accent). Just as he did with the question mark, the little ball at the end of sentences, Randall might have given us the clue that Beanish doesn’t have names for large numbers such as forty. You probably know where this is going, right? Megan had to explain arithmetically what is forty, and French works this way (well, mostly). A language derived/influenced by French might have inherited words such as quatre-vingts (four-twenties, also known as 80) or, in our case, five-eights.