Kwhazit has a comprehensive list of names for items and enemies and so forth, so I spent part of yesterday going through it to see whether any changes to naming were warranted. I found that it largely agrees with the GBA version on how to translate these things, so it seems nearly all of them can be left as they are without issue, because they are already accurately worded.
There were a few notable differences, so I did end up making some adjustments where they felt significant. Only a small number of items have been changed, but I did end up renaming somewhere around ten percent of the enemies to reflect the Japanese more closely.
Some of them are clearly nonsensical joke names, and changing them to something more straightforward doesn't result in the loss of any important information. Nonetheless I did try to port these over where I could. One enemy is called something like "Barf of Love" spelled backwards.
I ended up naming him "Evoltimov". Another was especially obscure: it is the word for 'bird', backwards and misspelled, followed by a division sign, followed by 'snake', again backwards and misspelled.
After much back and forth on whether this was even worth bothering with, I eventually settled on "Revo Ekans".
I haven't looked at the spell names yet, but I expect the situation there will be similar and not much will need to be done.
Chicken Knife asked about how well the story information is presented in the GBA version. Mato was quite consistent in his praise for how well it was translated, and if you play that version you'll get nearly all of it. There are a few things that aren't quite right, such as the 'Magitek' issue I mentioned earlier, and Kefka making eloquent remarks to Celes after she stabs him, when he's actually supposed to be freaking out and screaming/babbling incoherently. It also has some unfortunate things like Ultros making jokes about tentacle porn; and it translates Cyan calling Celes a "dog of the Empire" as "Imperial b--", which contextually feels off and should be more akin to calling her "swine" or something of that nature. There were probably a few other things like this that I don't remember off the top of my head.
My version deals with these things more straightforwardly and without the weirdness, so naturally I prefer it; but the GBA's issues are pretty minor overall and it certainly isn't wrong to play and enjoy that version. One of the things Mato often emphasized is that there isn't always just one valid way of translating things, and he tended to refrain from definitively stating that one approach or interpretation was unquestionably superior to another. I adhered to his assessment of the original script quite closely, but undoubtedly my own reaction to what he was saying would have affected the tone of the writing to some extent.
Anyway, we're probably looking at a version 1.2 in the near future, to incorporate some naming updates and additional text formatting improvements, and hopefully there won't be much more to do after that. I still want to actually play this thing at some point without looking for stuff to be fixed.