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While mind maps are not specifically intended for organising problems, I have used a variation of them many times when attempting to solve difficult problems with many constraints and they have worked out to be extremely well suited for the job. Start with the mind map keeping the problem in focus Mark the variables that may be critical to the problem ...
In many disciplines there often exists a set of solutions to a commonly occurring problems. In software and in structural architecture we call these design patterns. If these don't exist in your field you may want to begin a taxonomy of your own, share it with others, get feedback and develop it some more.
This might be a bit obvious or simple... but... Might it be an idea to make a overview of everything in excel? Here you can link part of the calculations relatively to each-other, but still have an overall scope of everything. You can even draw in it. Add definitions, and use those all again in the program. Hope it helps!
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