Have you read and completed all the requirements in the "How to play" section?
I only get this error when the original mod (Danymok's Vanilla Expansion) is not activated, but only when this submod is activated - https://youtu.be/b0ogDeBBq6Q

Also, after activating both modifications, make sure that this submod is HIGHER in the list than the original modification (as in the video).

Trying to start this mod and I'm getting a CDT error stating unidentified unit "helot" in
the building.txt file.

Is there a simple work around?

1. When attacking (regardless of who initiated the attack), you will control the faction you last controlled.
2. If you have an alliance (there's a forced diplomacy feature for this, so a second faction under your control agrees to any diplomatic requests) and you attack someone with one of your factions, you will control the faction that initiated the attack (provided that armies from different factions under your control were close to each other on the campaign map and entered the battlefield).

So0 what happens if both of your controlled factions try to manual battle?

The author of Danymok's Vanilla Expansion plans to add emergent factions in the future. I'll try to support this submod until emergent factions are released (because CMF can't work with emergent factions).