A good reference. "National Innovative Capacity", by Porter, M. and Stern, S., The Global Competitiveness Report 2001-2002; New York: Oxford University Press, 2001
I would also encourage you to study OECD innovation scoreboard, which can provide you with useful findings across countries. In this order, Oslo Manual provides some indexes.
Definitely look at the work by Sanjaya Lall on measurement, and also his critique of standard scorecards. He remains one of the definitive references for much of the industrializing world.
On actual technological capabilities and industrial transformation, one of the most detailed discussions is the UNIDO 2005 report which discusses their index in detail and why/how it's different from others and why the improvement is necessary to measure national capabilities.
For case studies of national capabilities from an institutional and evolutionary standpoint, hard to beat Richard Nelson (Ed.) National Systems of Innovation, and the work of Bengt-Ake Lundvall. On indicators you can also look at Danele Archibugi's work and that of Jorge Katz on Latin America.
On differences from the standard views on capabilities and why something else might be needed on models of innovation for developing economies, you can look at the work of mine with Judith Sutz (Srinivas and Sutz 2008), and Arocena and Sutz 2000, 2003 on Latin America and also recent work by Carlo Pietrobelli and Roberta Robellotti, and Raphael Kaplinsky.