I think I figured this out. I did a search and pieced together a couple of really good ideas.
1. Save a copy of your bookmarks, this is important because many tried this and lost them.
2. Turn off and DELETE all of your bookmarks on all of your devices but ONE.
For now one I will call it the Master. Make sure no strays stay behind.
3. On the Master, DELETE all bookmarks but don't turn Sync off. This is cleans up iCloud.
4. Turn off iCloud sync on Master, in this case it is my MacBookAir
5. Restore Bookmarks
6. Clean up Bookmarks
7. Turn Bookmark Sync back on the Master, this will push them to iCloud
8. On each device, turn sync back on. Verify each did it correctly
9. Do this for all devices.
Apple, you make this WAY too HARD by trying to be SIMPLE. Must be becase iCloud is not what was promised, your Dev's are in arms over how bad it is. Search for it.