What are some tools to effectively synthesize information from research?
For Qualitative coding and synthesizing of information, there are number of tools you can use (specifically addressing your concerns 1 &amp; 3):

NVivo


  NVivo is a powerful workspace for your qualitative analysis and mixed
  methods research offering tools so you can deeply analyze your
  unstructured data.


Leximancer


  Leximancer automatically analyses your text documents to identify the
  high level concepts in your text documents, delivering the key ideas
  and actionable insights you need with powerful interactive
  visualisations and data exports.


There are many other tools, but the above two are fairly standard practice among PhD/Researchers. Also, needless to say, they will require significant investment of time (if not financial - given most universities will have institutional subscription) and quite a lot of practice in order to use them appropriately.