established again and again that the eyes lay directly beneath mount Ihu and naho bay
Well, they do. The issue is whether the whole of each eye is entirely beneath them.
The way I aligned it in that pic, parts of each eye are under the proper spots. If you notice, the face design actually has the eyes very wide and the nose very narrow, so the island could actually be quite a bit smaller and still work.
I agree that keeping the numbers gives us an apparent inconsistency, but that's not really the main point -- the main point is that regardless of which "side" of the inconsistency we go with, Spherus Magna still ends up being incredibly huge, therefore gravity absorption is necessary.
(Also that the inconsistency isn't as extreme as it might sound without seeing it actually measured out.)
That's why inside metru nui, one of the suns was blacked out and the other was very dim. the eyes arent close enough together, even if they were "cross-eyed" to fit.
I'm not sure I'm understanding this sentence quite right, perhaps you could clarify? But Metru Nui's depiction would agree that the holes would have to be very "cross-eyed", regardless of the sizes involved, since the two holes were close together, a tiny percentage of the diameter of the dome. And it also portrays them as perfect circles, NOT the wide rectangles we see on the surface. So this is strong evidence that the sun-holes themselves are not synonymous with the entire eyes we see on the outside, and that if the holes were seen as the pupils, Mata Nui would indeed seem very cross-eyed.
But this is why I suggest it may be better to see them as the "tear glands" to the immediate right and left of the nose, rather than as pupils.
The whole geometry of the thing works out nicely that way, including with the official size numbers. 
The tiny island doesnt work with this,
How not? It's not as convenient as we all would have wished, but it does work.
and it contradicts the statement that the island was created to cover the face, which stuck out of the water
This need not be seen as a contradiction. Remember Greg's admonition to instead of complaining about apparent contradictions, come up with ways to make them work? (He made a whole mini-contest on the idea once, heh.) Under this theory, the face is indeed sticking out of the water, enough that the Kini-Nui sensors can work. Just not entirely out, and as far as I know, it was never explicitly confirmed to stick completely out.
And that wouldn't seem to fit the scenario of a crash-landing well anyways. Under normal circumstances, on alien worlds, maybe the island would be larger and he'd make the whole face stick out. (Although why? That just increases the likelihood of aliens finding it, so would seem to serve no practical purpose.) But a crash landing is not likely to fit so snugly. The Matoran are very lucky he didn't happen to land with his face entirely submerged by sheer bad luck. 
(on a subjective note, it also works against the visual poetry that the island was a mask all along.)
One word. Vahi. 
You're right, but we're talking about what we'd probably have to say if we were to reconcile all the canon facts, which is basically what this forum is for anyways. A fan fic can safely eschew whatever the author doesn't like, but this forum is for canon theories. It doesn't fit all that art with half the island and half a mask, but then those were always symbolic anyways (and somehow we never got the symbolism until near the reveal lol...).
I'm inclined to live with the inconsistancy if we can
Well, look, the canon HAS inconsistencies. It just does. But while we can live with them, it's certainly better to figure out how to make them not be inconsistencies. If we even care lol. 
I flatly disagree that we should consider later information that contradicts as a retcon of earlier stuff.
Well, I'm not saying this needs to be a retcon. In fact the only thing it contradicts, as that image pointed out, was "late stuff" -- that one scene in that one video. And BTW, it doesn't contradict the rest of the video, just that one tiny little scene -- given that there are even more blatant contradictions between various depictions of the robot and the planets and stuff in the final years, worrying about a few seconds in a non-storyline promo video wouldn't make much sense.
(Look at all the TLR depictions of craters on Aqua Magna for example, and the comic Spherus Magna at one point, all clearly contradictions.)
Anywho, my point was that IF this needed to be seen as a contradiction of early stuff, the standard policy in just about all fiction franchises is that later stuff retcons earlier. You can personally disagree for sake of fanfics and the like but in terms of canonicity that is what's generally agreed to do.
But it doesn't clearly contradict the earlier stuff, so moot point really. It contradicts a semi-late idea fans had that the island covers the face (myself included; I hadn't bothered to think about it), and a few seconds of one video, but nothing early.
It would be much better to just overlook the inconsistency for now, and come up with an explaination for it before we establish anything based on it. My personal preference is to take "40000000 feet" as a hyperbole.
Well an explanation for it is just what I gave. 
And hyperbole doesn't work, at least if I'm understanding your reasoning, unless you also see the size of Mata Nui Island as hyperbole too. But you seem to be saying that you think that size should be considered accurate. Right?
So, if we take the idea that the island neatly fits over the entire face (as seen in those few seconds of that video), then the robot is 2 million feet high rather than 4 million. Now how does hyperbole possibly fit with this? It's still impossibly huge, so to say that something is 2 million feet high still sounds like hyperbole to our normal ways of thinking.
Yet, it isn't close enough that you would ever reasonably round up to 4. If you have two cars, and someone asks you how many you have, are you ever going to say, "about four"? I mean, maaaaaaybe you could come up with some incredibly unlikely scenario, but overall, the answer is simply no. You might say "about three", but I doubt it. I would only think you'd round up to four if it was something like 3.5.
I also have another problem with trying to size down the robot that I forgot to mention -- if you did, the size of the continents would start to make the label "continent" unjustified. Mata Nui being so big, when compared with Earth, is good because Earth continents work out to be just about right for that. If he was half his size or less, they would seem more like just big islands. (At least if memory serves about that comparison. Maybe we should get another pic of Mata Nui next to Earth.
)
And again, are you saying this was hyperbole on Greg's part? Why would he do that? He told us canonically that it is that big. He didn't tell us that a character said it was that big, so I don't see how hyperbole could enter the picture anyways.
I'm not worried about the size of the planet. Its not something we ever really need to know specifically. but it would be illogical to think it's as big as jupiter. that's silly.
Er... why?
See again this pic:
http://biosector01.c..._Shattering.png
And actually, comparing with the difference between Jupiter and Earth, you could make a strong case that Jupiter is actually much too small compared to SM. See this pic for that:
http://upload.wikime..._Comparison.png
Now I'm willing to take the Shattering pic as a bit of artistic license, esp. given that it's from the Mata Nui Saga which had other known inconsistencies, but it would become quite absurd if it wasn't close to Jupiter's size... Right?
And that Jupiter/Earth pic actually looks about right under your "hyperbole" theory (2 million feet), maybe still a bit small, though.