So 5 minutes after I submitted this post, I managed to fix my problem.
Here is what I had been trying and how my solution came about.
- I noticed I had changed other cells and set the ignore flag on them
- saved my mod, closed the CK
- I restarted the CK, loaded my mod and the things I had copied appeared exactly where I had copied them as well as where I had placed them in my mod.
So I had 2 copies, 1st copy paste in a random spot so I could arrange them how I liked, and 2nd copy of where I had duplicated the rearranged items and placed them in my mod.
I had deleted the 1st copies after rearranging then duplicating and placing them appropriately in my mod.
- I noticed that I had FormIDs that started with 000...
- I noticed that they were all the 1st copies as explained above and had un-deleted themselves when I turned on the ignore flags for the cells I had unintentionally changed.
- I deleted all FormIDs starting with 000 except for my exterior world link and cell.
- I saved my mod and shut down the CK.
- I loaded my mod in the CK again
- The details sections still referred to cells being affected, the ones I had copied clutter from.
- I proceeded to pull my hair out trying to do the same thing over and over again.
- I then remembered that I am a scientist and as such I should step back from the problem and see the whole board.
- When I viewed those affected cells they appeared unchanged but the CK said that they had been modified.
- I looked at the details section of my mod again and noticed the deleted items.
- I toggled the ignore flag on all deleted Refs and affected cells.
- I loaded my mod and saved it, then I shut down the CK.
- I reloaded my mod in the CK and Voila! I had a clean mod!
Put that in your pipe and smoke it!
*Vulgar language removed*