Hey z929669,
I am still taking a look at the issue, I believe its related to the fact that I only have the free Skryim AE CC content and not the paid $20 upgrade. I tried searching this forum for if there's a version of the guide or steps to follow that support removing/not having the paid CC content, but could not find anything.
Because I don't have the CC content it looks like the step patches are not working, and this is leading to a number of graphical bugs (again, my fault not the guides). I am going to see if I can figure anything out while I wait for the AE upgrade to go on sale. I also need to figure out a way to patch in the CC content without having to redo step... I hope.
Thanks for the quick response, and if I come up with anything I will post here