I eventually solved this via the silent sql server installer with SkipRules parameters, a whole lot of them:)
/QS /ACTION=UPGRADE /InstanceName=MSSQL2012 /IACCEPTSQLSERVERLICENSETERMS /SKIPRULES= Engine_SqlEngineHealthCheck Engine_OnlySupportedFeaturesUsedCheckSystem Engine_OnlySupportedFeaturesUsedCheckUser Engine_SqlEngineRestartCheck EditionUpgradeMatrixCheck RebootRequiredCheck /IAcceptSQLServerLicenseTerms