The biggest pitfall I see in this area is the tendency in practice to confuse industry mass for a functioning cluster. You can go back to Michael Porter's original work and he offers great descriptions of how interrelated networks of firms and suppliers in an industry function as clusters but methodologically he left a lot for us to infer. Even where the work is good and people are doing more than just pointing to the presence of an industry in their region and calling it a cluster the result there has been some diversity of approaches. The references below may be of some help. Several of them are drawn from a special edition on cluster methodology that Economic Development Quarterly published in 2000.
I would also shamelessly like to plug some work on our website.
http://www.upa.pdx.edu/IMS/currentprojects/neo.html This includes a cluster monitor template for analysis based on the methodology we used in a series of studies of clusters in the Portland region. The studies, also at that link, include semiconductors, nursery products, creative services, lumber and wood products among others.
Good luck!
Austrian, Ziona (2000). Cluster Case Studies: The Marriage of Quantitative and Qualitative Information for Action. Economic Development Quarterly. 14:1, 97(14).
Economic Development Administration (1997). Cluster-Based Economic Development: A Key To Regional Competitiveness. Department of Commerce: Washington.
Fagan, Jocelyn H. (2000). Do Northeast Ohio's Drivers Derive Competitive Advantage From Shared Labor. Economic Development Quarterly. 14:1, 111(15).
Fesser, Edward J. and Edward M. Bergman (2000). National Industry Cluster Templates. Regional Studies. 34:1, 1(18).
Held, James R. (1996). Clusters as an Economic Development Tool: Beyond the Pitfalls. Economic Development Quarterly. 10:3, 249(13).
Hill, Edward, and John Brennan (2000). A Methodology for Identifying the Driver's of Industrial Clusters: The Foundation of Regional Competitive Advantage. Economic Development Quarterly. 14:1, 65(32).