BOOM!!! I've fixed it! To anyone else having this issue, here are the steps I took to resolve it... I hope you have a pre-Unity 5 upgrade back up!
1. Open project in Unity 4.6
2a. Delete NGUI folder as well as NGUI folder in "Plugins" if you made one
2b. Create a prefab of the NGUI instance in your scene (this step may be unnecessary)
3. Save Scene and Project
4. Open project in Unity 5 and let upgrade commence
5. Re-download/import NGUI from asset store and move correct folders to "Plugins" if needed
6. Close Unity and re-open project
at this point when I re-opened the project I got errors telling me that scripts and an API I'm using were outdated and needed to be upgraded. I had to close, reopen, and upgrade API twice before NGUI showed in the toolbar
7. Drag NGUI prefab back into hierarchy. This step seems unnecessary as subsequent scenes without the prefab rendered text correctly. It was a precaution I took because the upgrade process takes a bit of time and I didn't want to have to redo the whole thing.
8. Pour a glass of scotch because two years of hard work isn't completely borked.
step 8 is option but highly advised
The issue of text disappearing in the scene view remains, but compared to the original problem, it's negligible.
Hope this helps anyone with similar problems!