In Europe, twenty-four European Reference Networks (ERNs) work on rare disease registries in different clinical domains. The European Joint Porgramme on Rare Disease (EJP-RD) is working with these network members to assist in their transition to FAIR data, and the subsequent joining them together into a "Virtual Platform". This paper discusses a survey of the participants to identify their challenges in moving towards FAIR data publishing, identifying 41 unique FAIRification challenges which were categorised into “training”, “community”, “modelling”, “implementation”, and “legal”. Eleven solutions were then proposed, that can be implemented via improved guidelines, formal training courses, explanatory "games", and/or informal meetings between data hosts and FAIR experts. This work shows that a dedicated team of FAIR data stewards is an asset for harmonising the various processes of making data FAIR in a large organisation with multiple stakeholders. Additionally, multi-levelled training activities are required to accommodate the diverse needs of participants.