What are some tools to effectively synthesize information from research? Does anyone know any good, effective tool that people use to synthesize large amount of information from research?

By "tool" I am referring to softwares or practices that effective researchers use to: 

1. retain/recall large amount of research information,

2. progress quickly into a completely new field, 

3. find parallels between different concepts and fields

At the moment, I am basically going through papers one page at a time at a time, jogging down the keywords, trying my best to understand their derivation and result before proceeding to the next. 

There are several flaws with my current methodology. 


I write everything on paper, and paper pile up plus it is exhausting to write things down by hand 
I tend to lose track of prior results as I progress deeper into a subject, I would like some sort of review.  
I keep coming back to the same concept but only defined in slightly different contexts
I keep all the papers I find in one spot but have no way to reference them using any other tools, this means in a
few month I will have to trace back to the authors who wrote this or
that


I would like something to help me become more effective at quickly gather new information but at the moment I am hesitant to compile everything under the sun in a Microsoft Word or type everything in Latex but if that is the state of the art in the research community then I will begin my research compilation today!

Don't hesitate to share your ideas :) I will place a bounty on this question
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.