I would start with:
- Shibboleth log to find out what type of assertion coming, if there is any error during statup of shibboleth velocity templates and what actually being sent to SP at this moment ( after applied modification ) : https://www.gluu.org/docs/gluu-server/4.2/operation/logs/#adjust-shibboleth-log-level
- oxTrust log: to find out what "Custom NameID" change doing at this moment: https://www.gluu.org/docs/gluu-server/4.2/operation/logs/#oxtrust-logs