Q.What are Organic Weed Killers or Methods to kill Morning Glory Vines?
I have been fighting these for several years. Not allowing to flower or picking them. Removing the seed balls as soon as possible. Digging up the new ones. Spraying and/or painting weed killer on the leaves.
I am about ready to sell my house to get away from the menace and are not very fond of my neighbors for planting them on the fence between our properties. Thankfully they moved but unfortunately the Morning Glories stayed.

Certified GKH Gardening Expert
It would seem that you are doing the best that you can already! With persistence, you may win the battle, but it may take years. You can pour boiling water on the seedlings as they come up.
This article will help: https://www.gardeningknowhow.com/ornamental/vines/morning-glory/control-morning-glory-weeds.htm