"Is the 'case-study method' widely accepted as a methodology for a PhD in the business faculty"
YES
"What is the appropriate number of cases required in a PhD thesis?"
This cannot be answered generally. I employed a single-case study. More important is the process of defining units of analysis.
"Any sites/references/structure for writing up the methodology section using case-study approach?"
Probably one of the most often cited and "traditional" starting point is: Yin, R. K. (2003) Case study research and methods, 3rd edition, London:Sage