Battle command pointers and general question

I don't have time to go into your first question now, but I've got quick answers for you other two.

For the Magitek/Swdtech mechanic swap: yes. it is doable by moving pointers. I would have to work through it to make sure everything affected was taken care of, but definitely yes. What should work is to first find the command pointers and swap the two, then in the individual command codes, change the pointer for the first ability. Then swdtech should be set unless you want to reorder the spells in an order that makes more sense to the chargin mechanic. In the new swdtech you will have to build a command list based off the first ability pointer, its all in the dissasemblies. Search for Magitek in C1 or C2 (forget which right now).

For this, I would say just edit the palette from the editor rather than trying to use an external program. I forget if FF3usME does this, but SpriteEd definitely does.