As promised, here are some things that we can learn from the Vocabvlario da Lingoa de Iapam even if we don't really speak Portuguese.

Let me note before I begin that this is not intended to be a comprehensive survey of 17th-century Japanese, or even of all the implications of the issues raised in this post. Although I provide some context and supporting information from other sources, what I want to do here is to show what the orthography of the VLI shows, or at least suggests, in and of itself. It's all an excuse to type up some early 17th-century Portuguese as faithfully as possible, is what I'm saying.

1. Word-initial <f>

This is probably the most obvious point of interest in the VLI. First, here's some background:

Kana	Pre-reform kana	NJ	Meaning	OJ	Man'yōgana (example)
はな	はな	hana	flower	pana	波奈 (MYS 0816)
ひと	ひと	hito	person	pito	比等 (MYS 0808)
あわ	あは	awa	millet	apa	安波 (MYS 3451)
かい	かひ	kai	shell(fish)	kapi	可比 (MYS 3709)

(NJ = "Contemporary Japanese", the Japanese of today as opposed to the "Modern Japanese" that stretches back for centuries. OJ = "Old Japanese" as usual.)

Comparing the NJ to the OJ forms, we see that:

• Intervocalic /p/ became /w/ before /a/, and disappeared before all other vowels.
• Word-initial /p/ became /h/.

So what do those words look like in the VLI?

• Fana. Nariz. (78)
• Fito. Homem, ou molher. (96)
• Aua. Painço, ou milho, húa das cincº ſementes, ou legues chamados. (15. This actually appears capitalized as AVA because it is the first entry in its section; I took the liberty of normalizing to lower-case.)
• Cai. Ameijoa, ou outro mariſco do mar ſeme lhante. (33)

OJ intervocalic /p/ has already vanished, except where it has become /w/ before /a/. This is exactly the same as the contemporary Japanese we speak today. But word-initial /p/ hasn't become /h/. It's written <f>, and there are arguments over how it is to be pronounced. The simplest explanation is that it is an unvoiced bilabial fricative (i.e. a "weakening" of the original unvoiced bilabial plosive), but there is contemporary evidence against this — for example, Diego Collado's 1632 Ars Grammaticae Iaponicae Lingvae notoriously says:

Litera, f, in aliquibus Iaponiæ prouincijs pronunciatur sicut in lingua Latina; in alijs autem ac si esset, h, non perfectum: sed quodam medium inter, f, &, h, os & labia plicando, & claudendo, sed non integrum, quod vsu facilè compertum erit: v.g. fito.

The letter f is pronounced in various regions of Japan as it is in Latin. In others it is pronounced as if it were an imperfect h. For both pronunciations the lips and the mouth should be nearly, but not completely, closed. (Richard L. Spear's translation)

Since Latin <f> is supposed to have been labiodental, not bilabial (here I would insert a reference to Allen's Vox Latina if I had my copy handy), many interpret Collado's "sicut in lingua Latina" as evidence that <f> may not in fact have been unambiguously bilabial. Or, of course, Collado may have been misunderstanding something, writing as he was in that benighted age before even the first edition of Ladefoged's A Course in Phonetics had been published.

Whatever <f> was, it must have evolved into NJ /h/ after this dictionary was written. The whole story is rather more complicated and obviously can't be deduced from a single 1603 dictionary. Moving on!

2. Y before E

Some more background:

Kana	Pre-reform kana	NJ	Meaning	OJ	Man'yōgana (example)
まえ	まへ	mae	front	mapye	麻敝 (MYS 4129)
えだ	えだ	eda	branch	yeda	延太 (MYS 3603)
えて	えて	ete	get(ting)	ete	愛弖 (MYS 806)
えみ	ゑみ	emi	smile	wemi	恵美 (MYS 4106)

And then look how they appear in the VLI:

• Maye. Diante, ou em preſença, ou dantes. (154)
• Yeda. Ramo. (320)
• Yete. He como aduerbio, modo de fazer algũa couſa bem, ou por cuſtume, &c. (322. This also appears as <Ye, yuru, yeta> on 319, but I wanted a form that matched the MYS citation; and yes, <yuru> instead of <vru> is odd; see Doi et al 814-815 for more on this.)
• Yemi. Alegria, ou ſorriſo. (320)

In fact, as far as I can tell there are no instances of a mora consisting solely of /e/, with no initial consonant, in the dictionary. There are no words written starting with <e>, for example.

One interpretation of this would be that when the OJ distinction between /ye/ and /e/ was lost, the survivor was /ye/, and this didn't become /e/ until very recently — recently enough for the beer brand "Yebisu" (pronounced /ebisu/) to retain that initial <y> in its official English spelling, for example.

Frellesvig, however, rejects this interpretation. He argues that the /ye/ - /e/ distinction collapsed to /e/, and that what we see in the VLI is an additional rule that inserted an "on-glide" whenever /e/ appeared in a mora with no initial consonant. This sounds a bit fiddlesome, but it is in fact more parsimonious in many ways than the hypothesis of long-lived /ye/. For example, Frellesvig's explanation frees us from the need to devise a spaghetti of historical rules explaining how /pye/, /ye/, /e/, and /we/ all ended up as something spelled <ye>; instead, we can simply hypothesize that they all eroded down to phonemic /e/ which was then expressed with an on-glide (Frellesvig 208-210).

3. W before O

Similarly, there are no words starting with <o> in the dictionary. All the ones you might expect to start with <o> start with <uo> instead, and the same goes for word-internal moraic /o/:

OJ	NJ	Meaning	VLI
oto	oto	sound	Voto. Som, ou ſoido. (285)
wotokwo	otoko	man	Votoco. Homē varão, ou macho. (285)
awo	ao	blue/green	Auoi. Couſa de cor azul eſcuro. Itē, de Verde. Item, Verde. i. Que não he maduro. (16)
kapo	kao	face	Cauo. Roſto. (44)

(Note that <V> here is simply a capital <u>. Also note that I'm using the entry <auoi> instead of <auo> solely because the only definition given for the latter is a color that horses can be. Same morpheme, though.)

Frellesvig considers this basically the same phenomenon as the <ye> issue: a range of morae eroding down to /o/, which is then expressed with an on-glide.

However, one important difference from <ye> is that there is a loophole. The best example is probably:

• Vô (modern /oː/ "big", OJ /opo/)

Here, the second /o/ (the result of the intervocalic /p/ disappearing as discussed in point 1 of this post) has merged with the first one, producing a single long vowel. The two morae now form one syllable, and, logically enough, there is no need to interrupt the syllable halfway through to add an extra on-glide.

4. An extra vowel

Speaking of <Vô>, check these dictionary entries out. All of them, in modern Japanese, would be pronounced /koː/.

• Cǒ. Obediencia de filho pera o pay, ou mãy. (52) [孝]
• Cǒ. Adu. Aſsi, deſta maneira. (340) [斯う]
• Cô. Hum certo paſsaro grande. (52) [鴻]
• Cô. Exercicio, ou habito. (52) [功]

There's a systematic distinction being made between <ǒ> and <ô>. How it works becomes clearer when you look at the original (pre-reform) kana spellings of these words:

• 孝, 斯う = かう
• 鴻, 功 = こう

/au/ becomes <ǒ>, /ou/ becomes <ô>. What about words with the NJ pronunciation /Cyoː/?

• Qiǒ. Miyako. Cidade principal, ou corte. (198) [京, きやう]
• Qiǒ. Liuro. (198) [経, きやう]
• Qeô. [ve]l, qiô. Oje. (193) [今日, けふ]
• Qeô. l, qiô. Prazer, graça, &c. (193) [興, けう]

The rules appear to be:

• /au/ → <ǒ>
• /ou/ → <ô>
• /eu/ → <:iô>

Or we could skip the science and just read the VLI's front matter:

Nos vocabulos que tem acento longo como, Fiǒrǒ, Meǒji, &c. Eſcreuemos a primeira ſylaba ora por, E, ora por, I: & da meſma maneira os que tem o acento breue como Fiô, Qiô, &c. Por que poſto que na letra Cana, ſe eſcreuão huns, Fiau, & outros Feu: todauia na pronunciação não pedem mais, E, que I [...](ii)

In the words which have a long accent like "Fiǒrǒ", "Meǒji", &c., we write the first syllable now as "E", now as "I": & in the same manner those [words] which have a short accent like "Fiô", "Qiô", &c. This is because in the kana letters, [the former] ones are written "Fiau", & the others "Feu": however, the pronunciations do not call more for "E" than "I" [...] (My translation, after Doi et al 5)

That is, the acento longo of <iǒ> comes from kana spellings corresponding to /yau/, while the acento breve of <eô> comes from spellings corresponding to /eu/. Note the denial of any difference in pronunciation between <i> or <e> — it all comes down to <iǒ> vs <eô>.

The current thinking, by the way, is that <ô> was pronounced [oː] (you could see this as simple extension of the original /o/, at least in the cases where there was one), while <ǒ> was [ɔː].

References

• Collado, Diego. Ars Grammaticae Iaponicae Linguae. Rome, 1632. Project Gutenberg. Web. 12 March 2012. <http://www.gutenberg.org/ebooks/17713>
• Doi, Tadao 土井忠生, Morita Takeshi 森田武, and Chōnan Minoru 長南実. Hōyaku Nippo Jisho 邦訳日葡辞書. Tokyo: Iwanami Shoten 岩波書店, 1980. Print.
• Frellesvig, Bjarke. A History of the Japanese Language. Cambridge: Cambridge University Press, 2010. Print.
• Man'yōshū Kensaku Sisutemu Ver 2.2.0 万葉集検索システム. Web. 12 March 2012. <http://infux03.inf.edu.yamaguchi-u.ac.jp/~manyou/ver2_2/manyou.php>
• Spear, Richard L. Diego Collado's Grammar of the Japanese Language. University of Kansas, Center for East Asian Studies: 1975. Project Gutenberg. Web. 12 March 2012. <http://www.gutenberg.org/ebooks/21197>
• Vocabvlario da Lingoa de Iapam. Nagasaki, 1603. Tokyo: Benseisha 勉誠社, 1978. Print.

Other works cited

• Allen, W. Sidney. Vox Latina: The Pronunciation of Classical Latin. Cambridge: Cambridge University Press, 1965.
• Ladefoged, Peter. A Course in Phonetics. Orlando: Harcourt Brace, 1975.