How do you index packs into the scene/unit loader, so I can save my mod-based maps. Even saving mod-based maps with only ONE TYPE OF MOD ITEMS in the SAME MOD'S module, it crashes.

You're going to have to either: Include the .ini of the mod in question ahead of your scene in your scene's Index.ini OR include the .ini of the mod in question in the scenes.ini of your scene. (try looking in the middle section that says "Bunker Modules!"

And unfortunately, you usually won't be able to get away with including the Index.ini of the mod either. You'll probably have to dig a bit and find the .ini that directly references the bit you added to the scene. For example, for a ronin soldier, it would be:
IncludeFile = Ronin.rte/Actors/RoninActors.ini

Fortunatly, DSTech is very... messy, so the index already references EXACTLY the original files

Also, could I suffice by indexing all that stuff to the base.rte scene index?

You could, but then if you ever reinstall or move your scenes to a different installation, they will be broken again.