Update:
I have recently started school again (college classes) and I'm trying to get back to the project as much as possible (between classes and raiding in another game you might know of).
I have also recently started from scratch on a different method to the trees, going through the trees to find "filler" items in the trees in an attempt to find self-contained areas with more definite beginning and ending points.
Self-contained trees will most likely need to be put into their own subgroups, as the branches of the main trees are enormous. The filler items are items that don't really fit in with the other item types I have classified for the chart: magic, ability scrolls, medication, and ammo & tools (in the same group).
As of yet, I find an extended, searchable excel spreadsheet to be the most efficient and uncomplicated form for the game's refinement system; seeing as the number of items you can produce and re-produce are so convoluted.
I will continue to post updates as things happen to this project.
PS: I vaguely remember the policy on double posting... but can't remember exactly what it was. Is it alright if I post updates like this?