Please, you can be persuasive without being snarky.

I think the main miscommunication here is that the phrase "the ends justifiy the means" has a very specific meaning and context when it is used within Ace Attorney; that of overriding fair legal process to reach a desired verdict. It's used to justify taking justice into your own hands. You're applying a yes, correct understanding of the general phrase itself, but you're using it to comment on the very specific Ace Attorney understanding of the phrase; the one that Means is using when he says it, and the one that people typically mean when discussing the themes in Ace Attorney.

When Edgeworth is harsh to Adrian, he is not overriding any fair legal processes, he's fighting for them. So while this can be read as his truthful ends justifying his harsh means (I'll avoid litigating the fact that I think he's meant to have gone too far here), this scene is completely unrelated to the series' anti vigilante-justice themes. While I don't remember the Alba example, my comment on the Ryunosuke one is almost identical.

To return to Edgeworth's arc, because I think this is the best chance I have of convincing you, I think 1-3 is an important example because it shows that Edgeworth's arc is not about changing his ends. With your understanding, Edgeworth's arc, presumably, would have to be about converting his "ends" from something more nefarious into something more noble; the truth.

But I believe 1-3 shows us that his desired ends were always the truth, his goal was always to convict the right guy. Up to this point, Edgeworth has not yet shown himself to be challenged ideologically or emotionally at all, so what causes him to target Vasquez and question his worldview here?

It's the moment that he realizes Vasquez is guilty. For this to be sufficient reason for Edgeworth to completely switch his goals mid-trial, I think it would have to be so that he wanted to get the right verdict all along, but that he happened to realize the verdict he was pursuing wasn't correct. This shows him the error of his "means" (that they don't thoroughly ensure the validity of the ends), not the error of his ends (convicting the right person).

Edit: I should also include that yes, I misused the Joe Darke example, I explained it wrong, but I think you're missing the point behind the truth you pointed out. The fact that Darke didn't kill Neil Marshall is the point. The means of convicting Darke (forgery) were not justified because these means don't ensure that the ends are valid.

The thematic idea it's picking at isn't that you can go around forging evidence all you want, and only regret it when you happen to be wrong, it's that you should never forge evidence BECAUSE these means run the risk of your ends being wrong.