Wow.  This is something I never expected: a crossover with Amber and, well, /anything/.

First things first.  You use a lot of ellipses in your writing.  The vast majority of them in this story could have been replaced by other punctuation more appropriate.  I'll comment on them as I encounter them.

Also, (and this is extremely minor), you might want to add a [Fusion] tag to the subject line; it makes it easier for the readers to know what to expect.

A strange yet familiar tongue issued from the dreamer's lips in the
depths of the dream.  Not the Farsi of her homeland or the Japanese
she'd come to learn (albeit badly) from the residents of her new home.
"It won't be much longer now," she said in the odd tongue she somehow
could understand, though she couldn't recall ever having learned it.
"Only a couple more hours and I'll be going away..."

The ellipsis here seems to work, as it is the ending of an entire thought with the ending being omitted.

The manager/custodian sighed as if burdened with some throughly
undeserved task and trudged towards the basement with a toolkit.

I think you mean 'thoroughly' instead of 'throughly'.

Why
did this have to always happen to him?  He'd done everything that was
expected of him, he'd passed his entrance exams, he'd gotten into Toudai
and he'd even managed to narrow down the possible girls he'd made that
oh-so-sacred promise to from the entire female population of Japan to a
pair of pretty girls.

Since what follows "everything that was expected of him" is a list fo things expected of him, you could change the comma following "him" to a colon.  I think that would work better than a comma.

"Nooooo!" finished Keitaro as he landed in the water with a spectacular
belly-flop, that tossed up a huge wave, inundating the area.

The comma between "belly-flop" and "that" shouldn't be there, but the sentence sounds odd without it.  Howzabout "landed in the water with a spectacular belly-flop, tossing up a huge wave and inundating the area with water."  Or something to that effect.

Thus.. Did peace return to the onsen, the water stilling as the sound of
the insects and birds returned to their normal cycles.

"Thus did peace return..." would work much better.

In a matter of
moments it was as if no-one had ever bathed in the onsen before; Naru
and Keitaro were nowhere to be seen.

I can't decide whether "In a matter of moments" is a dependant clause that should be marked with a comma or not.  The mental debate goes back and forth in my mind.  Make your own decision on this one; I'm just voicing my thoughts.

Several long seconds passed of
this tranquil and total silence passed before the typical madness that
gripped the inn returned with the surfacing of Naru as she gasped
desperately for air.

The double use of the word "passed" really throws things off.  I'd suggest completely deleting the second one.

He descended though a thankfully open
window to crash land, face first, into a chair sitting at a table being
cleaned by his aunt, Haruka.

I think you meant to say "He descended through a thankfully..."

#Incomplete Scene Edited Out Temporarily#

This scene needs some work.  ^_~

The hot water heater.. if you could really call the mechanical
monstrosity he'd been forced to work on a heater.. was fixed, so Keitaro

The phrase between "if you could...a heater" would better be set off with a dash (--) or with commas; ellipses don't work well here.

What a throughly lousy way to begin a day that had been...

Again, you seem to mean "thoroughly", and I think a simple period would better end this sentence.

At least, soon, classes would begin and he would finally be able to see
some sort of true progress in his life.  He as free of the vestiges of

You forgot a "w".  "He was free of the..."

those he'd grown up with in school.  Or.. could it be more like he was
returning to his old friends after being away for a very long time?

If you want a slight pause there, I'd suggest using a comma instead of the truncated ellipsis.  Otherwise you could flat out delete it and have nothing but a space separate "Or" and "could".

The samurai stepped carefully to the side, narrowly avoiding a
cannonball from Suu as she dove into the water at full tilt, the little
Arabian's towel sailing up to find it's way onto a bush, the same bush
it always managed to get tangled in.

I just realized that this is a rather long sentence.  You might want to break it up after "full tilt" and rewrite the following sentence so it works grammatically.  The other comment I have is with "find it's way".  The proper use in this case is "its"; "it's" is the contraction of "it is", and "its" is the possessive.  This is one of the two words in the English language that I can think of that are opposite the standard rules, the other being "who" (who's -> contraction, whose -> possessive).

"Soaking..."

The ellipsis works here.  She's leaving other things unsaid, but not unthought (to herself).

Suu oh'ed softly and nodded up and down, shaking her entire frame in the
process and churning up waves in the water.

I know that "oh'ed" is the wrong way to write that, but I just can't figure out a better way of writing it.  Unless someone else can think of something better, I guess you may as well leave it.

"Ne, ne, ne, ne..." the child started, pitching her voice as if asking a
question as she circled round the swordswoman at a rather impressive
RPM.  "Um.. Could I sleep with you tonight?" she asked after a moment's

The first ellipsis is fine, but the second one should probably be a comma instead.

question seriously for several breaths before simply nodding.  "If you
require my presence to sleep.." she mused, "I shall endeavor to be of
assistance..."

The first ellipsis should be a comma, and the second a period.

Wherever the hell it was that the strange little girl was from...

I think that the ellipsis works here, but others might disagree.  *shrug*

Recently though, especially after the comedy of errors that had been the
trip out into the Pacific to retrieve Keitaro in time for him to submit
his application for Toudai, her nightmares and homesickness seemed to be
returning.  She could always tell.  She would wake up and try very hard
not to cry out, not wanting to wake her up.  The samurai could make out
a change in breathing pattern just as readily as a blood-curdling
scream, especially in the middle of a still night where the most common
sounds were the burbling of hot springs and the prowling of stray cats.

You have a lot of ambiguous antecedents in this paragraph.  So many, in fact, that I'm not quite sure what you're saying; I can't offer an alternative way of writing the paragraph.

She couldn't really read the odd little girl, but Motoko was certain
that Suu was holding something back.  She hated to use the term 'woman's
intuition' but it was just about the only thing left to her to explain
the slightly.. off.. feeling she'd been getting from Suu.

I've seen other ways of writing that pause that humans so often use in speech and thought, but I don't think I've ever come across a rule stating how it should be written.  Most often, I've seen it written with commas, but if you want to use ellipses then that should work, too.  However, if you do decide to use ellipses, you should use them in a trio instead of a pair.

Ultimately, something would be done...

Something had to be done...

They seem to work fine here.

Motoko stood up from the bath and, with a cautious check to make sure
Keitaro wasn't about to drop out of a tree.. or orbit.. or roll out from
behind a strategically placed rock, she quickly changed from her
dripping towel to dry off and threw a robe about herself, wrapping her
hair up in a towel to dry the rest of the way.

The phrase "or orbit...placed rock" is obviously something that you've set off, but you'll want to be consistant with whatever punctuation you use to set it off.  You ended it with a comma, so you might want to think about starting it with a comma.  Or you could use a dash to set the whole phrase off.  Either way, you shouldn't start it with an ellipsis, and you shouldn't have an ellipsis after "or orbit"; that one should be a comma.

About halfway back to
her room she heard the normal sounds of the inn become briefly
interrupted by the opening of a door, by its sound and direction the
front door.  "Just in time..." she remarked to herself drily as she
turned and made her way into her own little refuge.

A comma would work better instead of the ellipsis, but I think that either would work.

The manager came in through the front door and deposited his shoes in
the foyer.  "I'm home!" he announced, getting muted, feminine giggles
from the direction of the springs in reply.  "Oh.. never mind.." he

The ellipsis after "Oh" should be a comma, and the one after "mind" could work, but it should be a trio instead of a pair.

replied tiredly as he made his way into the inn proper and made his way
to his room.

You used "made his way" twice in the same sentence.  Deleting the second one and making no other changes makes the sentence sound awkward, so a rewrite looks to be in order.  I'm not quite sure what would work best.

It'd been a long, tiring day and he made it as far as his
futon before collapsing bonelessly upon it and veering sharply off into
unconsciousness.

"he made it as far as..." is an independant clause; there should be a comma after "tiring day

On the subject of the troubles of youth...

Since you're using this sentence, well, fragment as a transitional one, I guess the ellipsis would work.  Seemt to work from my POV, anyway.

"The truce is over now, you know..." Naru observed as the sounds of the
night settled down on the room.  The creeking of insects and the
settling of the wooden-frame building as the air around it began to
cool.

The ellipsis works here.

Her rival sighed a little and nodded.  "I hate making a competition out
of it," she mused in reply.  She shifted a little under the covers and
continued.  "Too bad there doesn't seem to be any other way to settle
this..."  She yawned and then peacefully nodded right off to sleep, a
rather impressive trick to manage in the middle of a conversation.

Here, too.

"I guess...." Naru began, then finding herself cut off by a nice
rumbling snore from Mutsumi.  "Oh, never mind..." she finished.

And the first one here works as well, but I'm not so sure about the second one.

Her occasional roommate, however, had much greater problems involved
with achieving a state of sublime unconsciousness...

Again, the debate rages in my head.  I can think of reasons for and against using an ellipsis here.  Personally, I wouldn't.  But then, this isn't my story.

It was time for sleep again and Koala was terrified of the notion.
She'd been running around all evening, steadfastly trying to keep
herself up and alert so she wouldn't fall asleep.  All she'd succeeded
in doing was wear herself out; leaving her huddled up in her futon, eyes
all but propped open in an effort to stay awake longer.

The semicolon doesn't work here.  A comma would be better.

It was a sensation somewhere between something entirely unlike having
her brain beaten out by a gold bar wrapped in a lemon peel and having
her eyes seeped in gasoline and lit alight.  A writhing network of
strands of.. something.. twisted round her with her at its center.  A
cacophony of sounds echoing in her mind increasing in pitch.  The
dreamself threw back her head, unfurled her wings (wings!?) and
screamed, the shriek echoing off of the unseen walls of the cavern
around her.

See my previous comment about the pause you have here.

When Motoko awoke to Koala's strangled cry, she found an empty futon by
her side.  It took the samurai all of three seconds to be out the door
in search of her missing charge...

I think the ellipsis works here, especially since this is the end of a chapter.  That's just me, though.

Overall, I liked this.  The unclarified references to Suu speaking Thari at the beginning and being grabbed by the Logrus at the end add a nice touch to it.  I'm still not sure who is supposed to be fused whith whom, (it seems, initially, like you have Suu being a daughter of Dara), but I'll enjoy finding out as I read it.  Keep it up.

Dar

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