Have a few hours in since updating to version M and no long saves or CTD and fast traveling is back to normal as well. However, I am seeing a new issue now and don't know if it is related or not but when I am in a settlement, I don't get the prompt to interact with Cait. I have to walk out of the settlement to get it appear. Haven't tried it with another companion yet so not sure if it is widespread.
Regardless, I would like to thank Kinggath and his dedicated team. I can only imagine the amount of code that had to be gone through to 1) write the mod to begin with, and 2) to repair its unwanted "features".