Man everybody wants to do a mostly rebels mod. Okay here's what happened with me - I've done a 'mostly rebels' mod of the early period w/c I do think 'feels right' - most events happen when they're supposed to - invasions of Wales and Ireland, squabbles over Aquitaine/Anjou, etc.

If you're getting a wrong units in a culture its probably because you have made an area into a rebel province but the units assigned to it were originally meant for another faction, lets say the Almohads. Mon ami, my guess is its probably Portugal or Cordoba or thereabouts - Almohad Spain whose culture is 'Christian' but is garrisonned by Muslim units. It happened to me and I ended up deleting a lot of non-harmful modifications before I discovered what was wrong. Basically you get Desert Archers and Berber Camels (I think) in Portugal. You must change this to something generic like peasants or spearmen or to Christian units. Otherwise the game will crash. Check out the other provinces and make sure the units match the culture!

Best of luck,
Gilbert de Clare