The second list there, that source doesn't cite their sources, so ... Well, a lot of them are just Japanese. The typical sounds of Japanese and Phantomilian are pretty distinct. Some of the most common Japanese sounds (ki, ka, no, chi, ku, ta, sa) don't appear at all in Stepping Wind, while W and F sounds appear much more in the song than in Japanese.
(Not very good at Japanese, heavily relying on the dictionary add-on here.)
ora yo (could be a mishearing of "hora!", "hey!")
iku ze ("to go" plus the emphasizer "ze")
choroi ze (easy/simple)
konna mon da ze ("konna mon" means "this kind of thing")
morattoku ze (not sure where the phrase comes from, but it's Japanese)
ikeru ze ("to be able to go")
temee (vulgar second-person pronoun)
rakusyo ("raku" is comfort/ease)
majikayo ("serious" + marker of doubt)
nani ("what")
yossya (or "yossha" in Hepburn, is the "Got it!" kind of "Okay!")
ite! (comes from "itai", "painful", because it's cool to turn "ai" and "oi" into "ee".)
sateto ("sate" is a conjunction meaning "now then"
doita (past tense of "doku", to step aside)
korya shitsurei ("korya" is a short "kore wa?", "what is this?", and "shitsurei" means "discourtesy" and is said to say one has been discourteous, like "excuse me".)
ikuzo (zo and ze are interchangable)
yarareta (past tense of "yarareru", to suffer damage)
The third list on the OP here, that's about what I'd like to be able to do ... Get the English and Japanese scripts and voice files from the games (don't know how to rip files, but transcribing everything would take more time) and compare them. And Phantomilian transcription is ... confusing. I have no idea what the difference between ルゥ (ru + small u) and ルー (ru + long vowel) is supposed to be. The guides show the Moo is ムゥ in Phantomilian. But there's the word トールン in Stepping wind with a long "o" in it, which is a different sound than ムゥ being transcribed as having a long "o"...
A few things from page 183 of the Famicom Door to Phantomile manual:
wafuu: the almighty word used in every situation. 1. Show affirmation, "yeah". 2. Question, "what?", "why?" 3. Show anger and uncertainty, "No!" 4. An expression of effort or shout used to encourage activity, "Heave-ho!" 5. a word for when you sigh. 6. An expression of surprise.
ra du: "yes", "I understand". Strong affirmation, like when a resolution must be made; used to show agreement with someone. "ruppu", in contrast, is a more carefree affirmation, like to signal to someone you're paying attention. wafuuradu: can be used together like saying, "yeah, I get it".
fia: first-person pronoun single subject, "I". "fia kuroa" I'm Klonoa. "fiirafuu kuroa", I'm Klonoa from the wind village.
fiaru: first-person pronoun plural subject, "we".
turappa: "thank you"
rekopanimuu: "you're welcome"
farudu: a word for when you're concerened for someone's health, situation, or feelings etc; "Are you alright?"
baramyuu: a word of apology
farutemanyuu: "to give it a go/take a chance with something"
farutu: "by the way"
rupuparamyuu: "don't say such unreasonable things"
rafimanyuu: Like the end of an eclipse, when something comes to light.
ramyuu: "waterfall"
(Interestingly, "rafimanyu", without the long vowel at the end, means something totally different in Stepping Wind.)
Words and stuff.