Since I don't know the origin of the Ubisoft game launcher copy of the game, I won't be deleting the steam copy. I have now transfered all the mods to the Ubisoft folder. I will delete them from the steam folder.
So far, everything is running smoothly. I launch from steam, it loads the Ubi launcher, and we are up and running.
If you just have the steam version, I'd check if you may have a Ubisoft folder with the game launcher in it. Just saying.
If your mods are working, great, no need to change things.