We followed a few principles of the so-called new Europeanisation research agenda. First, one should decouple formal rules from their practical application by focusing on actual changes to public administration. Second, it s useful to mix quantitative and qualitative methods in this analysis. Third, one should adopt a longitudinal approach to the study of public administration changes in order to follow the ‘bottom-up-down’ approach to Europeanisation (Graziano and Vink, 2013: 47). Fourth, it is important to compare PA across CEE countries in order to better disentangle the EU’s influence from CEE-specific factors. See our paper on the impact of the EU on agencification and depoliticisation in Lithuania on ResearchGate.
I ordinarily think of public administration as beyond my ken. But I recently made use of some of the EU Commission's progress reports on Turkey. The subject of administration comes up quite a bit. I realize that I am not quite answering your question, which focuses on methods of assessment, But it occurred to me that such reports on Turkey and/or other candidate members might be useful to you. See,for example, the 2014 report on Turkey: http://ec.europa.eu/enlargement/pdf/key_documents/2014/20141008-turkey-progress-report_en.pdf