In recent weeks I have procured a scientific victory from the PC-98 port, albeit in an emulator.
The game accepts English text for the customizable text boxes (civ name, leader name, city names), so that helped me keep track of what was going on where. I'm not exactly fluent in Japanese (I know some, but not enough to play a game without the help of machine translation), but after enough playtime I could remember what series of characters corresponded to particular units and buildings.
I have attempted to mess around with the customizable text files in the PC-98 version to varying results - just like the DOS version, you can change some of the game's text by editing the .TXT files (e.g. KING.TXT, ERROR.TXT).
Text files do not appear correctly in modern (Windows) text editors - or at least in the ones I use. I presume this is a text encoding issue that would not appear in a native PC-98 text editor. I recently acquired a PC-9821V7 (released circa 1995), but I'm waiting on a keyboard and mouse to get shipped, so testing on the real thing will have to wait until they arrive.
Changing the evolution cutscene text to English mostly works. The corresponding file is stored with the same layout as the DOS version's STORY.TXT. To test, I just replaced the original Japanese intro text with the text of the DOS intro. The resulting intro generally appears just as in the DOS version (though with the differing intro graphics). However, some of the transplanted lines did not appear correctly, appearing as more of a blob of pixels, and without the "shadows" that normally appear in the English DOS intro.
(Of note: The Japanese script font used in the port does not have these "shadows" at all (whether in the intro cutscene or in-game), probably because trying to put shadows on kanji/kana would not look great or be all that readable in-game.)
The text located in most of the other files are organized differently in the PC-98 version compared to the DOS version. There's no apparent labels (e.g. *LABEL) - each text box is prepended by some sort of NUL character.
Trying to replace the Japanese text in KING.TXT did not work at all, some text would appear in the wrong place (e.g. the "You failed the copy protection / manual check / Civilization Quiz" text appearing in place of the "Congratulations, you are now the leader of [CIV NAME], here are your starting technologies" text), while other text would run off the edge of the screen.
Some other files produced mixed results. In particular, some of the ERROR.TXT strings did appear correctly when replaced with English, while others did not.
After some testing, it appeared as if these messages are expected to be a specific length - if they are not, the text appears incorrectly. The encoding difference may have also been causing troubles.
(Random note: Some of the screens, particularly the opinion advisor and the spaceship screen, have text that runs into other screen elements, or off the screen edge, if your custom civ/leader/city names are too long.)