See, I forgot all about the multiple choices; I'd probably have just wound up confusing him.
One last thing: Once you have the player starting position set, save the scenario; it should default to your C3C scenarios folder.
Now open C3C. *Don't* open the scenario; start a normal game. Choose all the same settings your intended scenario is supposed to have, including difficulty level, victory options, barb and world settings, all of it.
Once you are at the starting screen with your settler ready to settle and all that, go to the main menu and choose Civ-Content (this is the scenario folder). Pick the scenario you just made in the editor and confirm you start as the correct civ in the correct place.
Save the 4000BC starting position so you have it later. Now you're good to go.
The reason why you have to load a normal game first with the same settings as your intended game is that C3C has a sort of bug: whenever you open a new game, the settings default to whatever you used immediately previously. With a normal game, this doesn't matter much as long as you pay attention (although it's the genesis of a billion 'why am I playing elimination in an epic game' questions on the forum), but scenarios can get messed up.
Good luck,
Renata