I started playing around with the tools gledson999 sent me, and finally got a bit more familiar with the process for editing graphics and for editing text, so I skipped a few steps from my last road map and went straight to the "Restoration" section: title screen, script, and audio samples.
Title ScreenThe obvious choice would've been pasting the american logo into the japanese title screen directly, but the american logo's shape, thick black outline, and colors didn't play together too well in the japanese title screen, so instead, I made a new one, keeping it as close as possible to the japanese logo. I took a similarly styled "Mega Man" text from a different source (the Mega Man X Command Mission logo) and adapted it directly into X6's japanese title screen.

For comparison, here are the original counterparts:

The title screen itself has been successfully inserted in the game with no issues (thanks blade133bo for helping me find the right files for the graphics and pallettes!). Picture above is an in-game screenshot.
However, as you can see, I still need to adjust the size and position of the "PRESS START BUTTON" graphic, which I also imported from the japanese version. The white italic text from the American one didn't work so well with this background.
Overall I'm very satisfied with the result, and plan to keep this as my default title screen (the one that goes into the standalone patch). As always, I'll leave it as a separate option in the Patcher, so you'll also be able to either keep the original american title screen or the untouched Japanese title screen.
After I figure out the "PRESS START BUTTON" part, I'll try replacing the logo on the loading screen for consistency (when using this version of the title screen).
ScriptI started some initial groundwork to insert DuoDynamo's retranslated script in, at least the main "cinematic" bits (that is, the text I'm not down right removing. I don't think I'll bother with Alia's in-stage calls). I've successfuly inserted single line edits, though I'm still in the process of figuring out how to recalculate pointers when increasing/reducing text length or number lines. Once I get to that point, it'll be a matter of fitting the text and scripting the whole thing.
Voice clipsI haven't made any real progress on this part, but as I've said before, I've at least confirmed the voice clips are still in the game. I hope I'll be able to track down the code bits that need to be restored from the japanese version.