I cannot recommend a suitable paper but I suggest you look at innovation in company organisation as a means to discriminate between these two concepts. In particular, if a new company does things differently and is successful they can change the theory of what makes a successful company organisation.
Antony, J. P., & Bhattacharyya, S. (2010). Measuring organizational performance and organizational excellence of SMEs–Part 1: a conceptual framework. Measuring Business Excellence, 14(2), 3-11.
The classic is Peters and Waterman "In Search of Excellence" - to me, you need to define what "excellence" is before you can differentiate between organizational excellence (which might refer to culture or strategic fit) and excellent performance (how well does the firm implement its strategy). Comments?