A fascinating feature of R’ Yaakov’s work are his linguistic studies. For example, he attempt to create an Egyptain etymology by pointing out that most Egyptain names contain as root letters the פ ר or ע (EY – Parshas Vayechi) See the discussion here.
He also notes that the letter ד must sound similar to the English “th” (as in “the”) as the Yemenites pronounce it for otherwise it would be impossible to lengthen the word “Echad” in Shema as the Halacha states (the d – dalet sound- cannot be lengthened and would sound like a d plus an extended a) (E”Y on SA in the notes). [1a]
An extensive discussion is in his בענין דקדוק קריאת שמע בכל לשון in EY to Seder Zeraim. There based on several diyukim in the Rambam demonstrating his usual critical style, he creates an extensive linguistic structure.
He correctly notes that there is a connection between the Latin and Hebrew alphabets  which he demonstrates like this:
A B C
ג ב א
Noting that the Gimel lines up with the C – He first suggests that the correct pronunciation of the Gimel corresponds with the s sound of the C (This he does based on the Gemara that compares Gimel to Tsadi – לא גמין צדיין)
However noting that the Latin C is spelled in Hebrew with a ק (Compare- Caeser – קיסר Ocean-אוקיינות Cedar-קדרום ) and therefore corresponds to a guttural G sound he recants. Instead he interprets the Gemara (acc. to the Rambam) as referring to the Greek names of these letters . He also interprets the line of the Gemara לא פיפין טיתין (whose Hebrew letters show little similarity) as referring to Theta and Pi . He writes that one cannot write Payin in Hebrew (for grammatical reasons) and therefore it is written פיפין.
In this a in his knowledge of History we see that despite a good grounding in the information on the subject, R’ Yaakovs sound innate critical sense alone suffices for him to make brilliant observations in an area far from his expertise.
(On a side note I refer you to the writings of HaRav Shir who suggests that the R was confused with an L among the Greeks (An example of this is the Chinese who pronounce an L as an R). See his interestng observations on Deucalion here. He further suggests that the Hebrew Ari became the Greek Leo. Again I can find no evidence to support this.)
[1a]In a somewhat similar deduction, R' Baruch Epstein observes that the Sefaradim are correct in pronouncing certain letters with a dagesh - else why would the Talmud need to warn that one pause between words with similar endings and beginnings (ליתן ריוח בין הדבקים) in the like of HaKanaf Pesil. The F and the P sounds are very different.
He would have been better served by making use of the Greek alphabet which is the intermediary between Hebrew (more correctly Paleo-Hebrew) and the Latin (Roman) alphabet. See this chart which I will make use of in my analysis.) Obviously lacking access to a Greek phonetic chart he had to make use of the Latin alphabet.
 In a note he mentions that according to this chart the Vav corresponds with an F (unclear in the chart). He then points out that the Sheimos HaGittin consistently spells names of the like of Freidel which should apparently be spelled with a soft Pey פ as וריידל with a Vav implying that a vav in fact had an F sound. He then points out that a German W is pronounce in English as a V and the German V as an F showing the overall relationship between these letters. And then explains the in Hebrew the W as in Vilna or Warsaw is spelled with two Vav’s – possibly similar to the W (double V)
 As you can see from the chart this is incorrect as the Greek Gamma in fact has a G not a C sound.
 The Gamin refers to Gamma. I do not know which letter he refers to with Tsadin. There is in fact no common greek letter corresponding to Tsadi – See the chart.
 I see no obvious similarity between these two letters. It would appear R’ Yaakov knew the names of the letters without being aware of the shapes. R’ Menachem Kasher in his analysis of the anointing of the Kohen Gadol with the Greek Chi in Horiyos (originally in article in a Sefer HaYovel whose name escapes me for the moment, also in the addenda to Torah Sheleimah Va’Yakhel) made use of the Shiltei Gibborim of Avraham HaRofe to identify the letters. I will include his analysis here for it is of interest in its own right –
He points to the Gemara in Horiyos that mentions the anointing of the Kohen Gadol in the shape of a Greek Chi (an X). (There some discussion if an X or some other shape see there). Why X? In Kesav Ivri (Phoenician) an X is a Tav, The Gemara in Shabbos mentions G-d telling the angels to paint a letter Tav on the foreheads for Tamus and Tichya. At the time of the anointing they were demonstrating to the Kohen Gadol that if he follows the correct procedure he will live if not he will die. Since there is no X in Ashuri they referred to the Greek letter instead. See also R’ Shaul Lieberman “Greek in Jewish Palestine” Pgs. 185- 190. My thanks to R’ S for directing me to this source.
R’ Yaakov also discusses this Gemara (See EY on Horiyos there) but lacking a complete knowledge in the Greek Alphabet is unable to find a good answer.