Since I have my own thread I had better post. I shall just put what I did:
After people said just try the editor, I did. In only a couple of minutes I made the changes to the AoD conquest I wanted (as highlighted by Civinator above) and everything worked as expected. I thought this is amazing, what tool is so intuitive that it allows you to do exactly what you want with no instructions? Amazing, as if Civ 3 needed any more amaze

Also it seemed to work well, in particular the native american civs seemed to get going much quicker making them more of a chalenge to the european civs.
I did have some problems/issues, if anyone has any feedback:
My second try was the Fall of Rome scenario, I wanted to make it Regicide instead of "loose 4 cities and die". I made it regicide in the Scenario properties, and selected "Automatically place Kings". However it did not give me king units, and I could not see an obvious king unit in the Starting Units list. Is there an easy way to make this change?
I also added workers using the method above, but it added them to a tile on the other side of the map to the rest of the units (I tested with the Vandals, and the workers were added in Turkey). How does one specify where the units go?
Am I changing the rules somehow without knowing it? In the AoD scenario I had a reasorce appear for the first time ever (a spices popped up in about Seattle). In the Sengoku scenario I removed the Regicide but added in the Shogun unit specifically, and the first time the Shogun fought another civ he got a promotion to Grandmaster, and the second time got a great millatry leader. It could be random, but would be quite a coincidence.
And it should go without saying,
@Samson , that if you mod the Sengoku scenario, you HAVE to use my own Japanese cities
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Linky?