I think my problem started when I had Dragonborn installed and then later removed it. I've put the DLSs back now. In some saves, but not all, mammoths or sometimes netches would appear out of thin air in some locations, even interiors. Outside I could see them fade into view and they would always make a beeline to me and either follow me around or attack me. Inside I would hear the attack music, my fsp would go very, very slow and mammoth legs or netch tentacles would be dangling through the ceiling. This has even happened with a new game. I've been attacked on the wagon ride to Helgen. It took me half a dozen tries before I got through that segment with no mammoths.

I've been dealing with it by going into godmode and then using "kill" to get rid of them when they do appear. I think the appearances might be lessoning. But is there anyway to get rid of them entirely?

Removing mods or dlcs and continuing that save is bad modding practice, i would suggest to start a new game and refrain from removing mods unless you can revert to a save prior that mod being installed.