Roofs aren't usually paper-thin. The tiles (or sheets, boards, or whatever else you plan to draw) have thickness, as does the (wooden/metal/plastic) understructure that they sit on. Thinking about the major parts that make up this roof should help you see where the lights and shadows can go.

I highly recommend looking at some reference photos for this sort of thing. Roofs aren't something you can draw well without having a basic understanding of how they work IRL.


Unrelated nitpicks, if you're interested:
The upper right part of the wall looks like it's at an angle because of the darker colours, but everything else suggests it's part of the same surface as the upper left.
The vending machine (?) seems to be facing in a different direction (mostly down to its width/depth ratio and the far side's white bit being much thinner than the near side's), but its stadow suggests that it's flat against the wall. The shadow of its legs also suggests the back of it is narrower than the front.
The air conditioning unit seems to be sitting a distance away from the wall because of where on the overhang it is. If it's meant to be attached to the house, it should probably be flush against the wall. If it's meant to be separated, then it could use a cast shadow to disambiguate this.
Speaking of cast shadows, that aircon pipe(?) looks pretty thick and should probably cast a shadow on the wall.
For an extra touch of realism, consider setting the doors and windows a little into the house rather than flush with the exterior wall, and perhaps raising the bottoms of the doors by a couple of pixels to show the threshold.

To me it reads more like squats than pain, because there's no sense of knockback or losing balance. Don't be afraid to put the character temporarily off-balance for the hurt animation!

Seconding MysteryMeat. With art this small, you're inherently simplifying and distorting things just to make them work at this size, which isn't great for learning anatomy. You should give yourself enough resolution/space that you can express everything as you see it, without forced stylization. That way, you'll learn anatomy rather than a version of it distorted in ways you weren't even aware of, and when you apply your anatomy knowledge to pixel art, you will consciously make the stylization decisions. Your art will look better for it.

Have you looked at the code? If it was done by a programmer worth paying, the ratio/sizing should be in there as variables you can tweak. If not, I could try taking a look at it for you, maybe I can figure it out and make it easier to edit for you. No one deserves to be beholden to such silly limitations xP

It's not anything specific I find overwhelming, the whole thing is just full of information, most of which means nothing to me. You need to reduce the information displayed simultaneously, I think.
(To be fair, this latest go is much easier to understand since it's just

Even with your description, it took me a while to figure out where the enemy dice were. I see now they're darker, but I tend to read things from top to bottom, so I expect the first thing to happen (enemy rolls) to be at the top. Having to refer to the chart on the other side of the screen is also slow and unnatural.
Consider:
- The enemy dice at the top of the page.
- The player dice at the bottom. The confirm/reroll buttons can be below or above, season to taste.
- A horizontal "scale" between the sets of dice representing the different hands, with little arrows above and below indicating where on the scale each hand is (enemy arrow from above, player arrow from below, the arrow colours should match the dice colour, so that both the colour and position correspond).  Every hand in dice poker can be assigned a unique point value, so a scale like this can even be used to distinguish similar hands (e.g. a pair of 2s versus a pair of 5s, the 5s can put the arrow slightly further to the right, indicating a better score). The hands should be indicated with icons rather than text.
- A bolt icon on the "Re-roll" button to make it clearer that it costs a bolt.
- Removing the little "frames" around the dice, they just add more meaningless visual information.
- Making the pips all the same size. Bigger pips make the dice read less clearly, as low rolls don't look empty. Bigger pips look like they're "stronger" than smaller pips, which is obviously not the case, they're weaker! The negative space around pips is important.
- Since my suggestion adds an extra visual element, it'll take up much more space vertically. To aid this, consider putting the player and monster portraits to the left of the dice rather than above them. I think this'll make them read more clearly anyway; I kept just parsing them as decoration.
- You could put a win/loss/tie indicator on the confirm button, that would make things even clearer. It would also avoid the need to make the player auto-win when they roll a win the first time, and the player could look over the dice as much as they'd like to understand how they won (dice poker can take some getting used to for players not already familiar with it).

This would be easier to parse IMHO, and more compact. It would leave the entire right page empty. If there isn't anything you specifically need the two-page set-up for, I'd reduce it to one page (with the wire binding on the top to make things more visually interesting, or on the side if you need it out of the way).

Using a scale with icons instead of text would also be easier to localise (or easier to understand for people whose main language isn't supported).
(Edit: You could make the scale easier to understand by putting the indicators in the middle of the hand's scale segment instead of weighted by score, and only do the weighting if both players have the same type of hand, to show which has the better score.)

Here's a quick mock-up of what a scale could look like:

You could have it bigger, mine's smaller than it should be. There's space! If you go for a single-page notebook, you could even make it large enough to include text labels, though IMHO you don't need them.
I used your blue palette but IMHO it would read better with some extra hues. The full house and straight are hard to tell apart with the colours currently available.
Some indicators of poor/great on the far left and right respectively could help players unfamiliar with dice poker.

Minor suggestions unrelated to clarity:
If you're doing a "pen art in a notebook" theme, consider avoiding even fills of the darker colours. Instead, maybe employ hatching or other indicators of texture to make them look more like pen drawings.
Give the dice slightly rounded corners so they look more like real dice. The interior already has rounded corners, it's weird that the exterior does not.
Your player and enemy dice should have the same spacing. The player dice are currently more tightly spaced.