Yes, from this description, it doesn't seem like any customization could have caused this issue.
Nevertheless, as I've mentioned earlier, it's hard to say what exactly went wrong without comparison with working instance that went through regular upgrade steps .
Maybe, before you go back to start, you could try to refresh class xml schema. Here is code example:
// get your document type dataclass info object
DataClassInfo dci = DataClassInfoProvider.GetDataClass("yourDoctypeCodeName");
// note it could be also possible to use GetDataClassFromDB("cms.file");
// set the dataclass table name to your custom created table name
dci.ClassTableName = "yourDBtablename";
// obtain class xml schema and form definition
string xmlXchema = CMS.DataEngine.TableManager.GetXmlSchema("yourDBtablename");
string xmlFormDefinition = FormHelper.GetXmlFormDefinitionFromXmlSchema(xmlSchema);
// assign the obtained strings to the class properties
dci.ClassXmlSchema = xmlSchema;
dci.ClassFormDefinition = xmlFormDefinition;
// Generate queries
SqlGenerator.GenerateDefaultQueries(dci, true, false);
But it's no guarantee, especially if you're missing some data in the DB.
Let me please know if I can be of any further help.