There is a difference between "keeping it close to the Japanese script" and "overlaying the Japanese grammar and sentence structure", though. I understand how hard you've worked on this script, but if you look at a sentence and can't naturally picture it being said that way in English (not counting words spoken in an unusual dialect or speaking manner), it deserves a revision - because the absolute most important thing to get across in either language is clarity.
For what it's worth, I agree with Dzumeister about the lines he pointed out as being awkward. His suggested changes are good, though I would use a few more contractions.
With the feedback of the last 10 days, we've made 5 revisions with hundreds of edits (V1.5 is the most extensive yet, should be ready tonight). Some are still looking at the V1.0 script. These changes should improve the experience substantially.
Some samples:
Before: Conveyed by the flow of water, I know of happenings throughout the world.
Now: The ebb and flow of water convey knowledge about events throughout the world.
Before: Randi! You have gained much strength!
Now: Randi! You've gotten quite strong!
Before: I've decided that I must ask you to leave this village.
Now: I've decided I must ask you to leave this village.
Before: As for things you can get here---there's nothing but Sea Hare's Tails...
Now: There's nothing to be found here but Sea Hare's Tails...
Before: Actually, the Great Viper struck Matsuketan down, our last king.
Now: Actually, the Great Viper struck down our last king, Matsuketan.
Before: ...but King Mammon had it sealed and henceforth, none may enter.
Now: ...but King Mammon had it sealed. Since then, no one's been allowed to enter.
Before: What lies there...I don't know.
Now: I...don't know what lies there.
Literal Japanese: What could be there...I know not.
Before: Oh, the Republic? They mostly live in a castle on the sea a bit west of here.
Now: Oh the Republic? Go a bit west of here, and it's the castle on the coast.
Before: It'll probably take time, but I'm certain she'll return to how she was.
Now: It'll probably take time, but I'm certain she'll be as good as new.
Before: A monster has moved into the Crystal Palace since there's no one else there.
Now: A monster has moved into the abandoned Crystal Palace.
Before: Show resolve!
Now: Hang in there!
Before: But it's lost its light, and its power is no longer befitting the legend.
Now: But it's lost its light, and its power is no longer worthy of the legend.
Before: And once you know which magic to use in the forest to the west...
Now: And once you know which magic to use in the western forest...
Before: Because I didn't want to die, I pretended that I had this illness. Share that with no one!
Now: Because I didn't want to die, I faked having this illness. Don't tell anyone!
The original opening:
ELLIOTT:RANDI, you doofus! If you're careless, we'll be found out and the village Elder will be angry yet again!
TIMOTHY:That's right. According to village rules, coming here is not allowed! I heard there was a ghost and stuff...
ELLIOTT:Pfft, the adults are the childish ones, huh? They say that because they think it'll scare us and we'll stay away. But...grandma did say that she saw a big light shining near the waterfall. Surely, there's an incredible treasure!
TIMOTHY:Now let's hurry and keep going!
The new opening:
ELLIOTT:RANDI, you doofus! If you're careless, we'll be found out, and the village Elder will be angry again!
TIMOTHY:That's right. According to village rules, coming here is not allowed! I heard there was a ghost and stuff...
ELLIOTT:Pfft, the grown-ups are the childish ones, huh? They think that'll scare us and we'll stay away. But...grandma said she saw a big light shining near the waterfall. There must be some incredible treasure!
TIMOTHY:We have to find it! Let's keep going!
etc. etc.
The V1.5 script is about 1.5% smaller than V1.0 with all of the new edits.