I am/was faced with similar both in my professional and personal projects. The only tool that I could aggregate everything I need to reference in it's native format was Evernote. While it is not perfect (def. not) it has been able to meet everything I need...the rest was developing a structure to tag, index, and funnel everything to something useful...I'm light years ahead now, but still polishing the terd shall we say....I hope maybe some day there will be a cross between Evernote and the power of Jupiter-like notebooks.