Honestly I don't think it's worth working with those clips. The intro scene isn't the only area where Working Designs made the clip significantly longer. There's a few other spots such as Ghaleon's death and what not where Working designs took a clip that was only say 20-30 seconds in the JP version and made it a whopping 1:05 or something if I remember correctly. That one is over 1MB in size and just wont fit, and there's not another existing file to split it into so you'd have to try and hack something in.
The XSeed dub's files are about the same length and file size as the original JP Saturn files so they all should just fit and work for the most part. The ones that are bigger will still fit into the buffer size if I remember correctly, they just wont work for just dropping it in with something like CDMage. There's also the fact that I'm using XSeed's dub in the FMVs since their dub matches the Japanese animation, unlike Working Design's dub which actually edited the animation to fit their dub. So there's also that aspect that works in the XSeed dubs favor along with the fact it's just easier to work with.
The converted XSeed clips can be found here:
Translating Lunar Silver Star Story