For the Magnet Train, MKDSCM has a neat tool that allows you to divorce textures from models and remarry them. I just modified the divorced textures with CrystalTile2 and remarried them afterward.
Out of curiosity, what was your hold up with the second image in the opening. Personally, I had encountered some bugs in the palette and had to reorder the whole palette. I don't have the best memory, so I can't remember exactly what I did.
On that note, I can't actually remember what I was going to ask you, but it is nice to know that someone else is actually working with HG/SS. I've only just begun to dig in, though, so I've a bit of work and experimentation ahead of me.