Hooray, I figured it out, you don't actually need to repack the files. The game engine will look at the local folder first.
Instructions:
1. Extract this from where the ExSTIAP.exe for P1 game resides, extract with folders.
You should have a ExSTIAP.exe alongside a ysbin folder and the yst0000.ybn files inside the ysbin folder.
Kouyoku Senki ExS-Tia P1, Eng MTL v1:
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If anything needs to replicate, skip all the complicated tools and just use GARBRO to extract the ysbin.ypf file and then use VNTranslationTools to translate.
I think there's a few issues with names inside text (I was fixing them when I went with Translator++ but that got messy so I went with VNTranslation and some Python script). The only real flub in this one is Nerdy Guy = Pick-Up Artist at the end.
This translation file is for Parallel 1 game. I don't know what the folder structure for the all-in-one game set looks like. I have them all separate.
edit: I'll say this translation is really, really rough. It has issues with the names going on the text fields and pushing text off the page. I'll see if it's an issue with me or bad support from VNTranslationTools. There's another route I can try as the person who wrote the tool for the first games has a YuRIS tool.
I have P3 translated too, but that's just as rough. P2 has an issue with crashing when playing.