Sadly I won't be able to do a full playthrough for some time, but here's what I've got so far -- mostly script nitpicks, but without further ado:
Script Nitpicks
*Recurrent problems with exclamation point distance in item acquisition messages.
*In Guardia Castle, 600AD, in one of the early events there, somebody says "Becareful..." Not sure which NPC it was now, but presumably someone encountered prior to speaking with disguised Marle.
*In Guardia Castle, 600AD, disguised Marle uses the words "atlast"; and "servents." Should be at last and servants.
*In Guardia Castle, 600AD, Lucca says "We don'tdon't want..."
*Manoria Cathedral, 600AD: One of the nuns uses the phrase "...tear eachother apart..." The words "each" and "other" need to be separated.
*I think when you step out of the Millennial Fair gate after the Manoria Cathedral quest Lucca says "I'd love too..." It should be I'd love to...
*Just after getting to 2300AD (In Bangor dome IIRC) Lucca says "We definately..." Should be "we definitely"
*In 2300AD, Ragged Old Woman in Arris Dome uses the phrase: "Death Peak. There needs to be a closing quotation mark. I.e., she should say "Death Peak."
*In 2300AD, the Guardian says after defeat: "Security Mode 7 deativated." It should be deactivated.
*In 2300AD, upon meeting Robo, Lucca says: "It's a bipedled humanoid robot!" That should be "bipedal".
*In 1000AD, when you visit Melchior's hut prior to the Heckran Cave quest, he reports that "There's also a passage to back to Truce..." ; delete the extra "to." Also, the word "deity" may be misspelled in his text.
*In 600AD, after Zombor, the Knight Captain says "We would certainly not survived" -- should read "We would certainly not have survived," though I might recommend "We certainly would not have survived."
*In 600AD, after Zombor, Robo says: "Please to meet you" to the Knight Captain. Should be "Pleased to meet you."
*In 600AD, a Young Woman in Dorino Inn says: A sword called "Masmune" was made ages ago. -- should be Masamune.
*In 600AD, a Young woman in (I think San Dorino's) Elder's House: Only the hero can wield it's power -- should be its.
Glitches
*The Naga Ette bromide room battle in Manoria Cathedral could use some pre-battle party repositioning if that's possible. My characters got stacked in very close proximity, but maybe the game always did that anyway.
*Lucca's Zonker-38 attack effect gfx may be messed up. She seems to shoot arrows with it.
*In Heckran Cave, the Djinn/Octoblush battle plays boss battle music -- is that intended?
*In Heckran Cave, I was able to actually bypass the Heckran battle by hugging a wall as I walked up to Heckran IIRC. Heckran gave his defeat dialogue and self-destructed on the spot. However, I fought Heckran normally after loading up a savegame, so I'm not sure whether it's random or if it's the way I walked up to him the first time around.
*You-know-who guarding the Magic Cave doesn't seem to have any dialogue...though maybe he's not supposed to be there at all when you're first able to access the Magic Cave.
*The Broken Hilt doesn't disappear graphically from Frog's floor when you acquire it, though it does get put into inventory correctly.
*Finally, there doesn't seem to be any battle music in Guardia Forest. However, I actually really, really liked fighting enemies and still having the peaceful forest theme going on for some reason.