Just a quick update.

So easypopulate would work fine If a category already existed it.
Issue seemed to be when creating new categories.
One work around was to create the categories manually and then uploading the spreadsheet...twice.
For some reason the first time would generate errors and only do a partial upload of new products. The second time it would be fine and upload everything correctly.

Anyways we are going to try and downgrade MySQL server later tonight back to 5.7 since we can't figure out what was going on. crossing fingers everything works after.