The Research methodology that I intend to adopt is Case study for one part and survey questionnaire for another. For case study, as per literature review and various forums, hypothesis emerge as findings and not for testing but for survey questionnaire the same are constructed
This of course depends on what you intend to find out. If you want to explain something (which, in my opinion, comes down to show how specific effects are produced from specific causes by one or several social mechanisms), then ideally, you would formulate and test hypotheses about relationships between causes and effects, and use case studies to identify the mechanisms that link them.
Having said that, I am not sure about hypothesis testing anymore after the whole approach of null hypothesis significance testing has been challenged, and convincingly so.
For m e, hypothesis for quants part and research question(s) for quals part. You need to frame each so there is a clear rationale, ie, does the quals build on results of qants?
It depends on the purpose, I think. However, from your question it is really not clear what you intend to do in your research. In qualitative you can propose some links between different constructs and then explore them empirically using a case study or other qualitative research methodologies. The use of methodology needs to be justified anyway. However, if you are trying to develop scale to be used later in your quantitative part, you do not form propositions; rather you simply focus on different concepts/dimension to include them as items in the measurement scales.
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