You're welcome.

Ah, that font suffers pretty badly from bad kerning, then. But yeah, good practice to draw it by hand. (Or at the least, pick a font without those issues and/or fixing those issues by hand when they occur)

Once more, you're welcome.

The reflection/lighting on that first vial suggests the light comes from more or less the frontal direction, by the way, while the shadow it casts suggests upper-left.

You're welcome. =)

Like I said, the mouth isn't bad, but I wasn't sure if it was intentional, so I figured I'd better say something anyway. =) Yes, you're right, the mouth is slightly ajar in the original sketch. The current pixel art doesn't read so much like slightly ajar as raised lip and snarling, but then, that seems to fit her personality, no? From what I can tell, she's not a happy-go-lucky lady, so...

As to the pose, it looks somewhat more natural, yes. The main issue remains albeit to a lesser degree. Her body twists in ways that might be possible but most certainly are not comfortable. Parts of her body suggest a perfect side-view, some suggest her body is turned slightly towards the viewer and others suggest she's turned slightly away from the viewer. The two areas dealing with the worst contortion are the transition from legs to torso and the upper torso/arms/neck area.
(Something about her feet also feels "off" to me, but it might be that's simply because the other issues are making it difficult to get a read on how she's supposed to be standing. Though I'm fairly sure her knee is not where her kneepad is unless she has her foot pretty far twisted inward at the ankle.)

For that matter, her arm-with-shoulder-pad is really off. With the way you've portrayed her neck, her shoulder should be a fair bit more to the (viewer's) right. Which also means you should show slightly more of the front-side of her shoulder/upper arm, and a fair bit less of the back-side.
The location it's in now is, I think, a left-over from the remarkable contortion of the original sketch, which showed off half of her upper back and half of her lower belly at the same time. (It's not quite that bad any more.  )

The shoulder-pad's angle also clashes with her arm's angle--it's not possible to bend your arm there, so as a result, it eh...sorry to be harsh, but it looks either like the arm's broken or like the pad is a cardboard-cut pasted on with some glue. 

There's some other anatomical issues as well, mostly dealing with the muscles on her legs and arms, but I'm not going to point those out for now, since the way to fix those depends on the way the pose itself is fixed, and pointing out issues that can't be solved yet doesn't seem particularly helpful to me.

The differences are not just facial features itself, but also the pose.

In the original pencil sketch, she's basically looking straight-forward to slightly downwards while her head's at an upward angle. More specifically, her chin is jutted up but her head is horizontally kept straight, which gives the whole "haughty" feeling: she is more-or-less literally looking down her nose on whatever she's watching.

In your pixel art, on the other hand, her head isn't upwards. It's cocked to the side. Just follow the line from one eye to another (or from one cheek to the other, etc.). That line's (nearly) horizontal in the sketch, but in the pixel art it's at what I'd estimate to be about a twenty-degree angle.

Her eyes, which in the sketch were looking slightly-down forwards are now looking sideways-up. Not because of the angle, but on top of it.

Furthermore, her chin and nose are more or less level with the viewer in the pixel art. In the pencil sketch, you can see some of the underside of the chin and nose.

You've also lost some of the sharpness/pointiness in the facial details from the sketch. Those aren't quite as important on their own, imho, but they somewhat helped amplify the sketch's haughty feeling.

For the most part, it's just a case of having smoother, less sharp curves and angles in the pixel art at various places, which is amplified by a fairly smooth, "round" shading. There are some more specific points that changed beyond that, however.
The shape of her eyes. In the sketch they're somewhat pointy towards the nose, whereas they seem to, if anything, get wider towards the nose in the pixel art. (they're also more lidded in the original sketch, as compared to the wide-open look from the pixel art, but I think that's mostly the pose-matter I described above)
The angle of her eyebrows. In the sketch, the eyebrows have a fairly sharp angle in them. This gives off the appearance of a slight frown or sneer. They're far smoother in the pixel art, following more of a gradual curve.