After I proved that it was NOT the SD card, I started deleting documents on internal storage. I have a ton of files synced to a cloud server.
I wasn't able to narrow it down to what file was causing it. I suspect it was a number of files.
I ended up renaming the folder that I sync to the cloud with a period on the front. As in ".Mobile Documents". That supposedly makes a directory 'hidden'. So far, the indexing service has not returned, and I am still able to access the files.
This may be a good fix, because it also hides some of my schematics and such documents from the Gallery, which I didn't want them to show up in the gallery anyway.