[dACE]

So I have studied the differences in more detail and isolated some custom routines.

The below routines can be implemented without messing with the colorization.
I have omitted one routine that I know mess with the colorization and some changes I believe were made to make the game compliant to real hardware.

ShadowOne333: If you want - go ahead and make the following changes to the EJRT patched rom and let me know if that made any difference:

---
2BAD: EA 00 21 -> CD 0B 00
---
000B:
00 00 00 00 00 00 00
=
EA 4E D0 EA 00 21 C9
---

---
2BC2: CD B9 3F -> CD 12 00
---
0012:
00 00 00 00 00 00 00 00 00 00
=
F0 41 E6 02 20 FA CD B9 3F C9
---

---
F040: 22 13 05 -> C3 90 00
---
0090:
00 00 00 00 00 00 00 00 00 00 00 00 00
=
F0 41 E6 02 20 FA 1A 22 13 05 C3 43 70
---

EDIT: avoid the last change, it will set the wrong palette for Samus when loading new background tiles.

---
23B2: CD 99 3F -> CD A0 FF
---

EDIT: One of the routines above fixes the artifact wall being generated when moving from one area to another.

/dACE

[ShadowOne333]

Sorry for the late reply, had a shitty weekend and couldn't work on anything hacking related.

I got back to it today and applied all the changes (except 23B2: CD 99 3F -> CD A0 FF because that one seems to be the one that changes Samus' palette between transitions). Don't know if this change in particular is the one you meant with this:

EDIT: avoid the last change, it will set the wrong palette for Samus when loading new background tiles.

However, I am still getting the artifact wall that appears when transitioning between areas.  All other patches have been applied and everything else aside from the artifact wall between transitions seems to be working okay, though I still have to test out the Ice beam and Queen metroid room.

With that said, if someone is reading this, I am requesting a Save File for Metroid II which is at the very end of the game so I can test the Queen Metroid bug.
I thought I had a 100% file on my Wii U but it seems that one was lost for some reason, so if anyone who is reading this has a save file at the end of the game, please share it so that I can test this faster. It would also help for testing the Ice beam palette as well.

[dACE]

Perhaps I can run some tests and see if I can figure out what routine fixes what problem.

I can also post the one routine I have omitted - maybe someone can figure out why it messes with the palette.

/dACE

[ShadowOne333]

I got a hold of a Metroid 2 save, now I can test the Ice beam, Queen Metroid and room transitions easier and faster.
I got up to the Queen Metroid and sadly, the flickering issue is still there, the Ice beam also doesn't change the palette of the enemies sadly.

I will keep making changes from what we have to see if something makes a difference.

[dACE]

Here are all the custom routines I have found with the corresponding HiJack:

Spoiler:

---
2BAD: EA 00 21 -> CD 0B 00
---
000B:
00 00 00 00 00 00 00
=
EA 4E D0 EA 00 21 C9
---

---
2BC2: CD B9 3F -> CD 12 00
---
0012:
00 00 00 00 00 00 00 00 00 00
=
F0 41 E6 02 20 FA CD B9 3F C9
---

---
F040: 22 13 05 -> C3 90 00
---
0090:
00 00 00 00 00 00 00 00 00 00 00 00 00
=
F0 41 E6 02 20 FA 1A 22 13 05 C3 43 70
---

---
3FD2: CD D9 3F -> CD 61 00
---
0061:
00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
=
C5 D5 CB 33 CB 32 7A E6 F0 83 5F 7A E6 01 C6 D2 57 FA 4E D0 F5 C6 20 EA 00 21 3E 02 E0 70 7E 12 3E 01 E0 70 F1 EA 00 21 EA 4E D0 D1 C1 C9
---

I have altered the last routine so it will not mess up the colors (C6 0B -> C6 20)

They seem to have no effect however - perhaps because the cartridge type must be altered as well.

/dACE

[ShadowOne333]

Here are all the custom routines I have found with the corresponding HiJack:

Spoiler:

---
2BAD: EA 00 21 -> CD 0B 00
---
000B:
00 00 00 00 00 00 00
=
EA 4E D0 EA 00 21 C9
---

---
2BC2: CD B9 3F -> CD 12 00
---
0012:
00 00 00 00 00 00 00 00 00 00
=
F0 41 E6 02 20 FA CD B9 3F C9
---

---
F040: 22 13 05 -> C3 90 00
---
0090:
00 00 00 00 00 00 00 00 00 00 00 00 00
=
F0 41 E6 02 20 FA 1A 22 13 05 C3 43 70
---

---
3FD2: CD D9 3F -> CD 61 00
---
0061:
00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
=
C5 D5 CB 33 CB 32 7A E6 F0 83 5F 7A E6 01 C6 D2 57 FA 4E D0 F5 C6 20 EA 00 21 3E 02 E0 70 7E 12 3E 01 E0 70 F1 EA 00 21 EA 4E D0 D1 C1 C9
---

I have altered the last routine so it will not mess up the colors (C6 0B -> C6 20)

They seem to have no effect however - perhaps because the cartridge type must be altered as well.

/dACE

Having the C6 20 creates a garbled mess in the game
Changing it to C6 0B does make the graphics appear okay, but the palette is mostly brownish.

And as you said, it seems like these changes to not have any effect other than what has been found so far.
The bugs present in the original hack are still there, even after the patches, so perhaps there's something else.
How does one check the cartridge type?

[dACE]

So I have solved this one now - here is what you have to do:

Move the palette definition
From: x8 4000 - x8 5000
To: x4 0000 - x4 1000

Move the palette data
From: x9 5000 - xD 4000
To: x4 1000 - x8 0000

Truncate the rom to 512 kB

Transfer all custom ASM and hiJacks from the fixed color-hack.

I also recommend the following:

Remove the back-wall in the final boss-room. It does not flicker anymore - but it does look better without it.

Redefine the palette for the suitless Samus in the best ending. I had to edit the sprite in order for it to look good (tweaked the eyes and bikini).

/dACE

[ShadowOne333]

So I have solved this one now - here is what you have to do:

Move the palette definition
From: x8 4000 - x8 5000
To: x4 0000 - x4 1000

Move the palette data
From: x9 5000 - xD 4000
To: x4 1000 - x8 0000

Truncate the rom to 512 kB

Transfer all custom ASM and hiJacks from the fixed color-hack.

I also recommend the following:

Remove the back-wall in the final boss-room. It does not flicker anymore - but it does look better without it.

Redefine the palette for the suitless Samus in the best ending. I had to edit the sprite in order for it to look good (tweaked the eyes and bikini).

/dACE

I'm a bit confused on the addresses.

So you mention this:

Move the palette definition
From: x8 4000 - x8 5000
To: x4 0000 - x4 1000

Move the palette data
From: x9 5000 - xD 4000
To: x4 1000 - x8 0000

For the first one, do you mean x8 4000 refers to address $4008 up to $5008?
Or what do you mean by x8 4000 - x8 5000?

Also, the "truncate rom to 512kb confuses me as well.
And by the ASM and hijacks, which ones do you mean?

The last two I can edit them once I find them in the ROM, but the rest of the info completely eludes me

Truncate the rom to 512 kB

Transfer all custom ASM and hiJacks from the fixed color-hack.

I also recommend the following:

Remove the back-wall in the final boss-room. It does not flicker anymore - but it does look better without it.

Redefine the palette for the suitless Samus in the best ending. I had to edit the sprite in order for it to look good (tweaked the eyes and bikini).

[redmagejoe]

I know this is kind of a necro, but I'm wondering if this ever received a finalization that would allow the hacks to work without color glitches on VBA-M or VBAGX? This seemed like the most relevant place to post.

Sorry again for the necro. It seems that someone made a hack to address this!

https://www.romhacking.net/hacks/4388/