"Gu" for the G tribe is just part of how spelling foreign words in Japanese tends to work. Their syllable-based alphabet often requires extra vowels to end up in the middle of words, but then they tend to skim over "u" sound and not emphasise it. In any case it's not an indication of the true pronunciation; they just can't get any closer. (For another FFXIV example there's Grynewaht – in Japanese, グリーンワート "Guriinwaat" – but again that's just the closest they can get to the European-based Roegadyn language.)
Meanwhile, Y'mhitra is "Ya'mitora" which again is extra vowels sneaking in for necessity, but we can gather that "Meetra" is the intended pronunciation.
Also, "Mi'quote" is an incorrect spelling that implies an incorrect pronunciation. It's Miqo'te, or Mikotte in Japanese – the "qo" is a "ko" sound so it shouldn't have a U in there, and the apostrophe is there to indicate that the "te" is a separate syllable.
