Thanks for the feedback Chetan.
We reverted back to 8.2, re-upgraded to v9, did the whole clear cache process. We got a "FINISHED" when reviewing the Event Log. However, we are still experiencing the same cmsapi 404 error with a blank dashboard.
We did notice another error in the Event Log attempting to access a missing /CMSWebParts/Viewers/Effects/lightbox.ascx (which I believe is removed in v9).
We added that file from v8.2, which made no real difference, and will adjust our webparts to the kentico blog post for it.