Have a good week off, then! I'll end up editing this post a bunch too for clarity's sake.
You can use Exit Stage in the intro stage, and this skips not only the intro stage, but Isoc's speech as well as the initial briefing at Maverick Hunter HQ, putting you right at the eight boss screen. I don't know if it's intended, but it definitely should stay in for those looking to jump right into the game proper. So far, there aren't any issues with doing this skip.
When encountering Zero Nightmare in Infinity Mijinion's secondary area, he asks "Zero... WHERE... is ZERO'?" with the apostrophe in there.
Central Museum as Zero:
(A bunch of these are to go with the ellipsis guidelines you posted before. I reserve the right to be wrong!)
Initial conversation with Alia "...the place is completely deserted." needs 'the' capped.
One random room "Alia? Great, the comm's off... what do I do now?" needs 'what' capped since it's the start of a new thought (arguably?).
Another random "Alia? ...the comm's dead?" needs 'the' capped.
Another "...this is getting real old real fast." needs 'this' capped.
Another "Again? Tch, what a pain... well, no use worrying about it." needs 'well' capped.
Zero VS Ground Scaravich "Oh-ho! If it isn't mister Zero, right back from the underworld." 'mister' needs to be capitalized since it comes before a name.
Alia's post-mission briefing says that Scaravich was rooting around "where Dr. Cain found you, X." even though you're playing as Zero. I'm not sure how to suggest rewriting this since you'd have to account for every player configuration (X only, playing as Zero, X with Zero unlocked). Is the assumption that X and Zero go through the stages together, just you only see and play as one? One of the great mysteries in the X series is what the other player characters are doing while you're in the field.
Later in the briefing, Alia says "...the worst part is that Gate didn't even bat an eye..." needs 'the' capitalized.
Back to the Central Museum proper, another random room has Zero say "...comm's dead... alright, then." Both 'comm' and 'alright' need to be capped.
Another "Oh no, not again... give me a break." 'Give' needs capped.
Another "The comm's dead... what the hell is going on?" needs 'what' cappped.
I noticed that both in the retranslation here and in the original English script, Dr. Light doesn't mention the spike immunity power of the Shadow Armor legs. I know it goes beyond the scope of the 'retranslation' part of the hack on top of being a feature request to mention it, but I just thought it odd that this fairly useful aspect is not mentioned anywhere. Especially since you can use the Shadow Armor legs as soon as you get them now.
There's severe lag during the dialog with Blizzard Wolfang in both the original and hacked version of the game. You're probably the best person to ask--what's causing that? It doesn't happen during the rematch in Secret Lab 3, but it still does if he kills you and you try again in North Pole Area. Weird!
During Zero's version of the 3000 souls cutscene (or at least the one where he interjects with a cut-in and everything; I got it as him at least), Alia says "...even it they were just a fake." 'It' should be 'if' here. During the same scene, Zero later says "Well, we can't be doing with a madman' pipe dream at a time like this." and it's missing the s on 'madman's'.
This happens in the original game too, but when using Zero's double-jump rolling slash with Z-Saber Extend equipped, the extension waves appear inside of his sprite erratically. I'm not sure if this can be fixed or is even a priority due to Z-Saber Extend having such a tiny additional range.
When entering Infinity Mijinion's secondary area with Zero, he says he senses something nearby and "...am I imagining things?" 'Am' probably needs capped.
When you talk with Dr. Light in that same area with Zero, he says "...you wouldn't perhaps know anything at all about me, would you?" and the first 'you' needs capped.
There are a couple of lines where they're not changed at all from the original game (X meeting Infinity Mijinion being one case). Are these worth pointing out, or were they deemed 'good enough' to remain?
Zero VS Infinity Mijinion: I'm not sure if the "clean up-- ...wait a minute" needs 'wait' capitalized (it's a new line of thought, right?), but "I'm sure I set up Illumina to guard this room! ...don't tell me--" needs 'don't' capped.
"W-WHAT'?" needs that apostrophe removed. I kinda feel that "how COULD you!" needs a question mark with the exclamation since it technically is a question.
Zero in Secret Lab: "...Alia? ...comm's already dead." after landing from the big hole; 'comm' needs capped.
X in Secret Lab: "...the communication's cut off already." needs 'the' capped.
There's something wrong with the terrain in Secret Lab 1 as of RC4. The first downward slope with ice on it has misplaced tiles that are oddly functional (didn't test the spikes), but the 'path' above goes nowhere.
You can get around the obstacles easily enough, but the map wasn't like this when I went through the game on RC3 the other day.
Zero meets Gate after Secret Lab 1: "...what? You used my DNA!?" needs 'what' capped.
"...you're completely insane!" needs 'you're' capped.
"Hah hah hah... now that's unusual." needs 'now' capped.
Zero VS Gate intro: "...are you telling me to simply give up?" needs 'are' capped.
Zero VS Gate aftermath: "...to think such an ancient program..." needs 'to' capped.
Sigma's first line has "!..." at the end, but I didn't cap the quote itself, sorry. 'D-don't be cocky' or something?
Zero's ending, Mysterious Scientist says "...so, according to my analysis..." and 'so' needs capped.
"...to be honest," later needs 'to' capped.
"...yes, I know." 'yes' needs capped.
"...yeah, I'm ready." 'yeah' needs capped.
"...got it." 'got' needs capped.
Well, that's once through with X alone on RC3, and once with Zero on RC4. I hope all of these help.