How Best To Put The Fact Jigsaw Together In Research The title to this question is the best way I can think offhand of phrasing it - but to anyone with a more widely accepted phrasing, please feel free to edit it.
Basically it's about a common experience in research where we have had all the requisite facts for some time (in some cases for years) but nonetheless miss viable conclusions that could yield opportunities to advance our work. As frustrating as the usual struggles of research are, the self-reproach felt after finally realizing something we could easily have obtained earlier is so much worse.
After one such occasion in my life, I had to ask myself hard questions about my research methodologies. I wondered if I had been unwise to ignore other research students' practice of keeping an index-card file. The index-card system was not simply a memory aid - it also allowed one to make multiple cross-associations between items of interest. Although perhaps 95% of the effort of maintaining an index-card system for one's research was in vain, the final 5% effort could save one's blushes.
More recently, reflecting on a research topic from earlier in my life, I came to a superficially counterintuitive but rationally interesting conclusion after putting 4 long-known facts together. Putting aside the suggestion of neglectful supervision of my research - I know few PhDs with genuinely adequate supervisors let alone ones who would constructively criticize the researcher - I have to wonder what would have been if newbee PhD candidates were first taught some means of collating their research facts and logically/sensibly constructing conclusions or exclusions from these.
May I ask PhD researchers here if today's academia provides any 'bootcamp' or practical methodologies for research reasoning prior to formally beginning their work ?
The methodologies I have in mind might be things like:

Writing out facts as premisses and trying to link them logically together
Sketching out concept associations or 'mind-maps' of facts or ideas
Speaking aloud some conclusions in the hope that, on hearing them, implications may be stimulated
Dialogues on blocking issues with a knowledgable colleague
Dialogues with common-sense people without expertise in one's research domain
That sherlock holmes trope where discoveries are made through some dispassionate application of pure crystalline logic is nonsense. If you want to do that you should be a protagonist in a fiction novel.
Turning disconnected facts into knowledge is creativity. If there was a universal tool for creativity we would all use it.